Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/inputs/xao Working: n-9-20.cluster.ucsf.bkslab.org:/scratch/xiaobo/83235/xao-8058115.15 Result: /scratch/xiaobo/83235/xao-8058115.15 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xao 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/xao mkdir: created directory `/scratch/xiaobo/83235' mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15' /scratch/xiaobo/83235/xao-8058115.15 /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/83235/xao-8058115.15/working' mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/protonate' Storing results in /scratch/xiaobo/83235/xao-8058115.15/finished Working in /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 /scratch/xiaobo/83235/xao-8058115.15/working/protonate /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Using inputs as protomers/tautomers. No processing done 467 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/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Bulk generating 3D conformations all protomers in /scratch/xiaobo/83235/xao-8058115.15/working/3D mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/83235/xao-8058115.15/working/protonate/xao-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 ZINC000619235507 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building' mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000619235507 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/1 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC3(F)F)CC2)cn1) `ZINC000619235507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000619235507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000619235507 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC3(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 16, 16, 8, 8, 1, 1, 1, 1, 4, 4, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/2 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/2' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC3(F)F)CC2)cn1) `ZINC000619235507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000619235507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000619235507 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC3(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 17, 17, 8, 8, 1, 1, 1, 1, 4, 4, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/3 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/3' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC3(F)F)CC2)cn1) `ZINC000619235507.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000619235507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000619235507 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC3(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 16, 16, 8, 8, 1, 1, 1, 1, 4, 4, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/4 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/4' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC3(F)F)CC2)cn1) `ZINC000619235507.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000619235507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000619235507 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC3(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 17, 17, 8, 8, 1, 1, 1, 1, 4, 4, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000619235507 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/finished' Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 Building ZINC000619235507 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000619235507 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 1) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC3(F)F)CC2)cn1) `ZINC000619235507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000619235507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000619235507 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC3(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 16, 16, 8, 8, 1, 1, 1, 1, 4, 4, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 2) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC3(F)F)CC2)cn1) `ZINC000619235507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000619235507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000619235507 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC3(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 17, 17, 8, 8, 1, 1, 1, 1, 4, 4, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 3) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC2CCC3(CC3(F)F)CC2)cn1) `ZINC000619235507.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000619235507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000619235507 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC3(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 16, 16, 8, 8, 1, 1, 1, 1, 4, 4, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 4) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/4: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC2CCC3(CC3(F)F)CC2)cn1) `ZINC000619235507.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000619235507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000619235507 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC3(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 17, 17, 8, 8, 1, 1, 1, 1, 4, 4, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000619235507 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 Building ZINC000619235507 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000619235507 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 1) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC3(F)F)CC2)cn1) `ZINC000619235507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000619235507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000619235507 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC3(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 16, 16, 8, 8, 1, 1, 1, 1, 4, 4, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 2) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC3(F)F)CC2)cn1) `ZINC000619235507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000619235507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000619235507 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC3(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 17, 17, 8, 8, 1, 1, 1, 1, 4, 4, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 3) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC2CCC3(CC3(F)F)CC2)cn1) `ZINC000619235507.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000619235507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000619235507 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC3(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 16, 16, 8, 8, 1, 1, 1, 1, 4, 4, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 4) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/4: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC2CCC3(CC3(F)F)CC2)cn1) `ZINC000619235507.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000619235507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000619235507 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC3(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 17, 17, 8, 8, 1, 1, 1, 1, 4, 4, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000619235507 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 Building ZINC000619235507 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000619235507 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 1) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC3(F)F)CC2)cn1) `ZINC000619235507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000619235507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000619235507 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC3(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 16, 16, 8, 8, 1, 1, 1, 1, 4, 4, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 2) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC3(F)F)CC2)cn1) `ZINC000619235507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000619235507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000619235507 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC3(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 17, 17, 8, 8, 1, 1, 1, 1, 4, 4, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 3) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC2CCC3(CC3(F)F)CC2)cn1) `ZINC000619235507.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000619235507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000619235507 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC3(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 16, 16, 8, 8, 1, 1, 1, 1, 4, 4, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 4) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/4: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC2CCC3(CC3(F)F)CC2)cn1) `ZINC000619235507.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000619235507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000619235507 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC3(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 17, 17, 8, 8, 1, 1, 1, 1, 4, 4, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000619235507 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619235507 Building ZINC000619372016 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619372016' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619372016 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000619372016 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619372016/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619372016 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/5 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc([C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3cccn3C)C2)c(O)cc1Cl) `ZINC000619372016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000619372016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619372016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000619372016 none Cc1cc([C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3cccn3C)C2)c(O)cc1Cl NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 1, 12, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [41, 41, 41, 17, 17, 17, 17, 17, 2, 1, 6, 1, 1, 1, 3, 3, 3, 3, 3, 17, 41, 41, 41, 38, 41, 41, 41, 41, 41, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 17, 17, 82, 41] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 158 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619372016 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619372016/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619372016 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/6 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/6' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc([C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3cccn3C)C2)c(O)cc1Cl) `ZINC000619372016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000619372016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619372016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000619372016 none Cc1cc([C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3cccn3C)C2)c(O)cc1Cl NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 1, 12, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 21, 21, 21, 21, 21, 3, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 21, 43, 43, 43, 34, 43, 43, 43, 43, 43, 21, 21, 21, 21, 4, 4, 4, 4, 4, 4, 21, 21, 86, 43] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 193 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619372016 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000619372016 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619372016/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619372016/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619372016 Building ZINC000619372016 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619372016' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619372016 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000619372016 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619372016/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619372016 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 5) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1cc([C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3cccn3C)C2)c(O)cc1Cl) `ZINC000619372016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000619372016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619372016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000619372016 none Cc1cc([C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3cccn3C)C2)c(O)cc1Cl NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 1, 12, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [41, 41, 41, 17, 17, 17, 17, 17, 2, 1, 6, 1, 1, 1, 3, 3, 3, 3, 3, 17, 41, 41, 41, 38, 41, 41, 41, 41, 41, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 17, 17, 82, 41] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 158 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619372016 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619372016/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619372016 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 6) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1cc([C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3cccn3C)C2)c(O)cc1Cl) `ZINC000619372016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000619372016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619372016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000619372016 none Cc1cc([C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3cccn3C)C2)c(O)cc1Cl NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 1, 12, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 21, 21, 21, 21, 21, 3, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 21, 43, 43, 43, 34, 43, 43, 43, 43, 43, 21, 21, 21, 21, 4, 4, 4, 4, 4, 4, 21, 21, 86, 43] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 193 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619372016 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000619372016 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619372016/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619372016/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619372016 Building ZINC000619384183 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384183' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384183 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000619384183 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384183/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384183 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/7 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C(C)(C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1) `ZINC000619384183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000619384183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000619384183 none COC(=O)C(C)(C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 47, 9, 26, 26, 5, 9, 5, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 9, 9, 9, 9, 9, 9, 47, 47, 47, 26, 26, 26, 26, 26, 26, 5, 4, 4, 1, 4, 4, 9, 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, 45]) total number of confs: 198 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384183 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384183/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384183 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/8 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/8' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C(C)(C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1) `ZINC000619384183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000619384183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000619384183 none COC(=O)C(C)(C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 47, 10, 28, 28, 5, 10, 5, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 10, 10, 10, 10, 10, 10, 47, 47, 47, 28, 28, 28, 28, 28, 28, 5, 4, 4, 1, 4, 4, 10, 10, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 202 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384183 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000619384183 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384183/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384183/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384183 Building ZINC000619384183 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384183' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384183 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000619384183 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384183/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384183 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 7) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC(=O)C(C)(C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1) `ZINC000619384183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000619384183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000619384183 none COC(=O)C(C)(C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 47, 9, 26, 26, 5, 9, 5, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 9, 9, 9, 9, 9, 9, 47, 47, 47, 26, 26, 26, 26, 26, 26, 5, 4, 4, 1, 4, 4, 9, 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, 45]) total number of confs: 198 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384183 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384183/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384183 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 8) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC(=O)C(C)(C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1) `ZINC000619384183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000619384183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000619384183 none COC(=O)C(C)(C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 47, 10, 28, 28, 5, 10, 5, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 10, 10, 10, 10, 10, 10, 47, 47, 47, 28, 28, 28, 28, 28, 28, 5, 4, 4, 1, 4, 4, 10, 10, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 202 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384183 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000619384183 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384183/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384183/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384183 Building ZINC000619384186 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384186' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384186 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000619384186 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384186/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384186 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/9 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C(C)(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1) `ZINC000619384186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000619384186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000619384186 none COC(=O)C(C)(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 47, 10, 28, 28, 5, 10, 5, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 10, 10, 10, 10, 10, 10, 47, 47, 47, 28, 28, 28, 28, 28, 28, 5, 4, 4, 1, 4, 4, 10, 10, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 202 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384186 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384186/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384186 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/10 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/10' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C(C)(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1) `ZINC000619384186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000619384186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000619384186 none COC(=O)C(C)(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 47, 9, 26, 26, 5, 9, 5, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 9, 9, 9, 9, 9, 9, 47, 47, 47, 26, 26, 26, 26, 26, 26, 5, 4, 4, 1, 4, 4, 9, 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, 45]) total number of confs: 198 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384186 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000619384186 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384186/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384186/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384186 Building ZINC000619384186 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384186' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384186 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000619384186 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384186/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384186 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 9) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC(=O)C(C)(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1) `ZINC000619384186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000619384186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000619384186 none COC(=O)C(C)(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 47, 10, 28, 28, 5, 10, 5, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 10, 10, 10, 10, 10, 10, 47, 47, 47, 28, 28, 28, 28, 28, 28, 5, 4, 4, 1, 4, 4, 10, 10, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 202 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384186 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384186/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384186 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 10) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC(=O)C(C)(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1) `ZINC000619384186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000619384186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000619384186 none COC(=O)C(C)(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 47, 9, 26, 26, 5, 9, 5, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 9, 9, 9, 9, 9, 9, 47, 47, 47, 26, 26, 26, 26, 26, 26, 5, 4, 4, 1, 4, 4, 9, 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, 45]) total number of confs: 198 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384186 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000619384186 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384186/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384186/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619384186 Building ZINC001119633718 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119633718' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119633718 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119633718 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119633718/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119633718 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/11 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(O)(Cc2ccccc2F)CC1) `ZINC001119633718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119633718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119633718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001119633718 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(O)(Cc2ccccc2F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 12, 17, 17, 17, 17, 17, 17, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 12, 12, 12, 17, 17, 17, 17, 4, 4, 4, 4] 150 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119633718 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119633718/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119633718 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/12 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/12' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(O)(Cc2ccccc2F)CC1) `ZINC001119633718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119633718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119633718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001119633718 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(O)(Cc2ccccc2F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 10, 17, 17, 12, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 10, 10, 17, 17, 17, 17, 3, 3, 3, 3] 150 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119633718 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC001119633718 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119633718/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119633718/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119633718 Building ZINC001119633718 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119633718' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119633718 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119633718 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119633718/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119633718 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 11) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/11: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(O)(Cc2ccccc2F)CC1) `ZINC001119633718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119633718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119633718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001119633718 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(O)(Cc2ccccc2F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 12, 17, 17, 17, 17, 17, 17, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 12, 12, 12, 17, 17, 17, 17, 4, 4, 4, 4] 150 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119633718 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119633718/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119633718 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 12) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/12: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(O)(Cc2ccccc2F)CC1) `ZINC001119633718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119633718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119633718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001119633718 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(O)(Cc2ccccc2F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 10, 17, 17, 12, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 10, 10, 17, 17, 17, 17, 3, 3, 3, 3] 150 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119633718 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC001119633718 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119633718/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119633718/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119633718 Building ZINC000619934119 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619934119' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619934119 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000619934119 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619934119/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619934119 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/13 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)N(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CCC2) `ZINC000619934119.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000619934119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619934119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000619934119 none COc1ccc2c(c1)N(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CCC2 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.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 14, 14, 9, 3, 13, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 14, 14, 14, 22, 22, 22, 14, 14, 14, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619934119 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619934119/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619934119 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/14 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/14' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)N(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CCC2) `ZINC000619934119.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000619934119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619934119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000619934119 none COc1ccc2c(c1)N(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CCC2 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.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 15, 15, 15, 15, 15, 15, 15, 9, 3, 15, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 15, 15, 15, 22, 22, 22, 15, 15, 15, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619934119 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000619934119 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619934119/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619934119/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619934119 Building ZINC000619934119 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619934119' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619934119 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000619934119 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619934119/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619934119 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 13) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc2c(c1)N(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CCC2) `ZINC000619934119.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000619934119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619934119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000619934119 none COc1ccc2c(c1)N(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CCC2 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.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 14, 14, 9, 3, 13, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 14, 14, 14, 22, 22, 22, 14, 14, 14, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619934119 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619934119/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619934119 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 14) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc2c(c1)N(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CCC2) `ZINC000619934119.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000619934119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619934119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000619934119 none COc1ccc2c(c1)N(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CCC2 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.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 15, 15, 15, 15, 15, 15, 15, 9, 3, 15, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 15, 15, 15, 22, 22, 22, 15, 15, 15, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619934119 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000619934119 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619934119/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619934119/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000619934119 Building ZINC000487431323 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000487431323' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000487431323 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487431323 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000487431323/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000487431323 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/15 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)(CC(=O)OC)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000487431323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487431323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000487431323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000487431323 none CCC(CC)(CC(=O)OC)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 8, 11, 8, 18, 27, 27, 27, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 18, 18, 27, 27, 27, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000487431323 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000487431323/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000487431323 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/16 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/16' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)(CC(=O)OC)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000487431323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487431323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000487431323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000487431323 none CCC(CC)(CC(=O)OC)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 8, 12, 8, 18, 27, 27, 27, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 18, 18, 27, 27, 27, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000487431323 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000487431323 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000487431323/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000487431323/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000487431323 Building ZINC000487431323 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000487431323' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000487431323 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487431323 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000487431323/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000487431323 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 15) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCC(CC)(CC(=O)OC)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000487431323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487431323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000487431323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000487431323 none CCC(CC)(CC(=O)OC)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 8, 11, 8, 18, 27, 27, 27, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 18, 18, 27, 27, 27, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000487431323 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000487431323/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000487431323 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 16) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCC(CC)(CC(=O)OC)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000487431323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487431323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000487431323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000487431323 none CCC(CC)(CC(=O)OC)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 8, 12, 8, 18, 27, 27, 27, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 18, 18, 27, 27, 27, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000487431323 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000487431323 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000487431323/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000487431323/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000487431323 Building ZINC000078124185 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000078124185 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/17 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(C)c3ccc(F)cc32)cc1) `ZINC000078124185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000078124185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000078124185 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(C)c3ccc(F)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 2, 23, 28, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/18 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/18' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(C)c3ccc(F)cc32)cc1) `ZINC000078124185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000078124185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000078124185 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(C)c3ccc(F)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 2, 23, 28, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/19 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/19' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(C)c3ccc(F)cc32)cc1) `ZINC000078124185.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000078124185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000078124185 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(C)c3ccc(F)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 1, 7, 7, 1, 1, 1, 2, 22, 27, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 7, 7, 7, 7, 7, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 7, 7] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/20 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/20' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(C)c3ccc(F)cc32)cc1) `ZINC000078124185.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000078124185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000078124185 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(C)c3ccc(F)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 1, 7, 7, 1, 1, 1, 2, 22, 27, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 7, 7, 7, 7, 7, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 7, 7] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000078124185 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 Building ZINC000078124185 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000078124185 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 17) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/17: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(C)c3ccc(F)cc32)cc1) `ZINC000078124185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000078124185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000078124185 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(C)c3ccc(F)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 2, 23, 28, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 18) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/18: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(C)c3ccc(F)cc32)cc1) `ZINC000078124185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000078124185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000078124185 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(C)c3ccc(F)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 2, 23, 28, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 19) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/19: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N2CCCN(C)c3ccc(F)cc32)cc1) `ZINC000078124185.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000078124185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000078124185 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(C)c3ccc(F)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 1, 7, 7, 1, 1, 1, 2, 22, 27, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 7, 7, 7, 7, 7, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 7, 7] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 20) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/20: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N2CCCN(C)c3ccc(F)cc32)cc1) `ZINC000078124185.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000078124185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000078124185 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(C)c3ccc(F)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 1, 7, 7, 1, 1, 1, 2, 22, 27, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 7, 7, 7, 7, 7, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 7, 7] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000078124185 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 Building ZINC000078124185 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000078124185 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 17) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/17: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(C)c3ccc(F)cc32)cc1) `ZINC000078124185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000078124185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000078124185 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(C)c3ccc(F)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 2, 23, 28, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 18) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/18: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(C)c3ccc(F)cc32)cc1) `ZINC000078124185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000078124185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000078124185 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(C)c3ccc(F)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 2, 23, 28, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 19) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/19: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N2CCCN(C)c3ccc(F)cc32)cc1) `ZINC000078124185.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000078124185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000078124185 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(C)c3ccc(F)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 1, 7, 7, 1, 1, 1, 2, 22, 27, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 7, 7, 7, 7, 7, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 7, 7] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 20) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/20: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N2CCCN(C)c3ccc(F)cc32)cc1) `ZINC000078124185.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000078124185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000078124185 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(C)c3ccc(F)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 1, 7, 7, 1, 1, 1, 2, 22, 27, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 7, 7, 7, 7, 7, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 7, 7] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000078124185 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 Building ZINC000078124185 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000078124185 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 17) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/17: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(C)c3ccc(F)cc32)cc1) `ZINC000078124185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000078124185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000078124185 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(C)c3ccc(F)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 2, 23, 28, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 18) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/18: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(C)c3ccc(F)cc32)cc1) `ZINC000078124185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000078124185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000078124185 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(C)c3ccc(F)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 2, 23, 28, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 19) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/19: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N2CCCN(C)c3ccc(F)cc32)cc1) `ZINC000078124185.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000078124185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000078124185 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(C)c3ccc(F)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 1, 7, 7, 1, 1, 1, 2, 22, 27, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 7, 7, 7, 7, 7, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 7, 7] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 20) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/20: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N2CCCN(C)c3ccc(F)cc32)cc1) `ZINC000078124185.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000078124185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000078124185 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(C)c3ccc(F)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 1, 7, 7, 1, 1, 1, 2, 22, 27, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 7, 7, 7, 7, 7, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 7, 7] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000078124185 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000078124185 Building ZINC000620226113 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000620226113' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000620226113 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000620226113 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000620226113/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000620226113 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/21 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccon3)CC2)cc1Cl) `ZINC000620226113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000620226113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000620226113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000620226113 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccon3)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 12, 8, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 4, 6, 8, 8, 8, 8, 26, 26, 26, 26, 8, 8, 2, 2, 2, 4, 4, 4, 2, 2, 8, 8, 8, 8, 8, 26, 26, 8, 8, 8, 8, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000620226113 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000620226113/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000620226113 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/22 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/22' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccon3)CC2)cc1Cl) `ZINC000620226113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000620226113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000620226113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000620226113 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccon3)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 12, 8, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 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: [6, 4, 2, 4, 4, 1, 1, 1, 2, 3, 5, 7, 7, 7, 7, 30, 30, 30, 30, 7, 7, 4, 4, 4, 6, 6, 6, 4, 4, 7, 7, 7, 7, 7, 30, 30, 7, 7, 7, 7, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000620226113 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000620226113 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000620226113/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000620226113/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000620226113 Building ZINC000620226113 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000620226113' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000620226113 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000620226113 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000620226113/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000620226113 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 21) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccon3)CC2)cc1Cl) `ZINC000620226113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000620226113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000620226113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000620226113 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccon3)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 12, 8, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 4, 6, 8, 8, 8, 8, 26, 26, 26, 26, 8, 8, 2, 2, 2, 4, 4, 4, 2, 2, 8, 8, 8, 8, 8, 26, 26, 8, 8, 8, 8, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000620226113 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000620226113/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000620226113 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 22) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccon3)CC2)cc1Cl) `ZINC000620226113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000620226113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000620226113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000620226113 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccon3)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 12, 8, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 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: [6, 4, 2, 4, 4, 1, 1, 1, 2, 3, 5, 7, 7, 7, 7, 30, 30, 30, 30, 7, 7, 4, 4, 4, 6, 6, 6, 4, 4, 7, 7, 7, 7, 7, 30, 30, 7, 7, 7, 7, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000620226113 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000620226113 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000620226113/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000620226113/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000620226113 Building ZINC000151650409 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000151650409' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000151650409 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000151650409 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000151650409/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000151650409 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/23 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)CCCC1) `ZINC000151650409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000151650409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000151650409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000151650409 none CCOCCC1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 35, 34, 18, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 34, 34, 34, 34, 49, 49, 49, 49, 49, 38, 38, 35, 35, 11, 11, 2, 2, 2, 4, 4, 4, 2, 2, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 153 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000151650409 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000151650409/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000151650409 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/24 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/24' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC1(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)CCCC1) `ZINC000151650409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000151650409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000151650409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000151650409 none CCOCCC1(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 40, 39, 21, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 39, 39, 39, 39, 48, 48, 48, 48, 48, 41, 41, 40, 40, 11, 11, 2, 2, 2, 4, 4, 4, 2, 2, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 145 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000151650409 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000151650409 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000151650409/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000151650409/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000151650409 Building ZINC000151650409 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000151650409' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000151650409 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000151650409 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000151650409/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000151650409 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 23) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCOCCC1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)CCCC1) `ZINC000151650409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000151650409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000151650409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000151650409 none CCOCCC1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 35, 34, 18, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 34, 34, 34, 34, 49, 49, 49, 49, 49, 38, 38, 35, 35, 11, 11, 2, 2, 2, 4, 4, 4, 2, 2, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 153 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000151650409 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000151650409/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000151650409 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 24) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCOCCC1(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)CCCC1) `ZINC000151650409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000151650409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000151650409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000151650409 none CCOCCC1(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 40, 39, 21, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 39, 39, 39, 39, 48, 48, 48, 48, 48, 41, 41, 40, 40, 11, 11, 2, 2, 2, 4, 4, 4, 2, 2, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 145 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000151650409 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000151650409 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000151650409/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000151650409/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000151650409 Building ZINC000170731019 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000170731019' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000170731019 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000170731019 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000170731019/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000170731019 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/25 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(c2ccncc2)n[nH]1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000170731019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000170731019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000170731019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000170731019 none O=C(Nc1cc(c2ccncc2)n[nH]1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 6, 5, 12, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 4, 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: [9, 1, 9, 24, 24, 24, 24, 49, 49, 49, 49, 49, 24, 24, 24, 1, 1, 1, 6, 6, 1, 1, 6, 6, 24, 24, 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000170731019 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000170731019/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000170731019 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/26 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/26' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(c2ccncc2)n[nH]1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000170731019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000170731019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000170731019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000170731019 none O=C(Nc1cc(c2ccncc2)n[nH]1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 6, 5, 12, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 4, 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: [9, 1, 9, 24, 24, 24, 24, 49, 49, 31, 49, 49, 24, 24, 24, 1, 1, 1, 6, 6, 1, 1, 6, 6, 24, 24, 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]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000170731019 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000170731019 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000170731019/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000170731019/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000170731019 Building ZINC000170731019 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000170731019' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000170731019 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000170731019 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000170731019/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000170731019 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 25) grep: /scratch/xiaobo/83235/xao-8058115.15/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(Nc1cc(c2ccncc2)n[nH]1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000170731019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000170731019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000170731019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000170731019 none O=C(Nc1cc(c2ccncc2)n[nH]1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 6, 5, 12, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 4, 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: [9, 1, 9, 24, 24, 24, 24, 49, 49, 49, 49, 49, 24, 24, 24, 1, 1, 1, 6, 6, 1, 1, 6, 6, 24, 24, 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000170731019 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000170731019/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000170731019 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 26) grep: /scratch/xiaobo/83235/xao-8058115.15/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(Nc1cc(c2ccncc2)n[nH]1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000170731019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000170731019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000170731019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000170731019 none O=C(Nc1cc(c2ccncc2)n[nH]1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 6, 5, 12, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 4, 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: [9, 1, 9, 24, 24, 24, 24, 49, 49, 31, 49, 49, 24, 24, 24, 1, 1, 1, 6, 6, 1, 1, 6, 6, 24, 24, 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]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000170731019 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000170731019 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000170731019/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000170731019/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000170731019 Building ZINC000427778903 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778903' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778903 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000427778903 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778903/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778903 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/27 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CC1CCCCC1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000427778903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000427778903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000427778903 none COC(=O)[C@H](CC1CCCCC1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 20, 3, 8, 8, 23, 27, 27, 27, 27, 27, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 20, 20, 16, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 3, 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778903 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778903/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778903 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/28 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/28' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CC1CCCCC1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000427778903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000427778903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000427778903 none COC(=O)[C@H](CC1CCCCC1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 19, 2, 9, 9, 25, 31, 31, 31, 31, 31, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 19, 19, 17, 17, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 2, 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, 44, 45]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778903 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000427778903 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778903/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778903/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778903 Building ZINC000427778903 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778903' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778903 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000427778903 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778903/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778903 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 27) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC(=O)[C@H](CC1CCCCC1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000427778903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000427778903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000427778903 none COC(=O)[C@H](CC1CCCCC1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 20, 3, 8, 8, 23, 27, 27, 27, 27, 27, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 20, 20, 16, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 3, 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778903 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778903/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778903 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 28) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC(=O)[C@H](CC1CCCCC1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000427778903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000427778903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000427778903 none COC(=O)[C@H](CC1CCCCC1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 19, 2, 9, 9, 25, 31, 31, 31, 31, 31, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 19, 19, 17, 17, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 2, 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, 44, 45]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778903 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000427778903 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778903/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778903/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778903 Building ZINC000427778910 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778910' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778910 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000427778910 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778910/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778910 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/29 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CC1CCCCC1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000427778910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000427778910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000427778910 none COC(=O)[C@@H](CC1CCCCC1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 17, 2, 8, 8, 23, 26, 26, 26, 26, 26, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 14, 14, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 2, 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, 44, 45]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778910 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778910/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778910 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/30 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/30' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CC1CCCCC1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000427778910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000427778910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000427778910 none COC(=O)[C@@H](CC1CCCCC1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 20, 3, 8, 8, 23, 27, 27, 27, 27, 27, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 20, 20, 15, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 3, 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]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778910 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000427778910 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778910/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778910/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778910 Building ZINC000427778910 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778910' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778910 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000427778910 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778910/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778910 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 29) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC(=O)[C@@H](CC1CCCCC1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000427778910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000427778910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000427778910 none COC(=O)[C@@H](CC1CCCCC1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 17, 2, 8, 8, 23, 26, 26, 26, 26, 26, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 14, 14, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 2, 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, 44, 45]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778910 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778910/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778910 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 30) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC(=O)[C@@H](CC1CCCCC1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000427778910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000427778910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000427778910 none COC(=O)[C@@H](CC1CCCCC1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 20, 3, 8, 8, 23, 27, 27, 27, 27, 27, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 20, 20, 15, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 3, 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]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778910 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000427778910 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778910/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778910/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427778910 Building ZINC000427957757 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957757' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957757 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000427957757 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957757/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957757 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/31 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCS1) `ZINC000427957757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000427957757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000427957757 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCS1 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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 14, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 24, 1, 29, 1, 1, 1, 4, 4, 1, 4, 4, 4, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 46, 46, 46, 46] 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]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957757 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957757/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957757 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/32 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/32' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCS1) `ZINC000427957757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000427957757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000427957757 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCS1 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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 14, 7, 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] 0 hydrogens 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, 27, 1, 32, 1, 1, 1, 4, 4, 1, 1, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957757 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000427957757 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957757/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957757/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957757 Building ZINC000427957757 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957757' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957757 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000427957757 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957757/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957757 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 31) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCS1) `ZINC000427957757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000427957757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000427957757 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCS1 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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 14, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 24, 1, 29, 1, 1, 1, 4, 4, 1, 4, 4, 4, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 46, 46, 46, 46] 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]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957757 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957757/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957757 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 32) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCS1) `ZINC000427957757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000427957757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000427957757 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCS1 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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 14, 7, 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] 0 hydrogens 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, 27, 1, 32, 1, 1, 1, 4, 4, 1, 1, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957757 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000427957757 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957757/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957757/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957757 Building ZINC000427957762 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957762' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957762 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000427957762 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957762/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957762 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/33 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCS1) `ZINC000427957762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000427957762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000427957762 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCS1 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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 14, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 22, 2, 31, 1, 1, 1, 5, 5, 2, 5, 5, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 105 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957762 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957762/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957762 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/34 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/34' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCS1) `ZINC000427957762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000427957762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000427957762 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCS1 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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 14, 7, 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] 0 hydrogens 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, 23, 2, 32, 1, 1, 1, 5, 5, 1, 5, 5, 5, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 5, 5, 5, 5, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 103 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957762 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000427957762 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957762/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957762/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957762 Building ZINC000427957762 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957762' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957762 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000427957762 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957762/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957762 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 33) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCS1) `ZINC000427957762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000427957762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000427957762 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCS1 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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 14, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 22, 2, 31, 1, 1, 1, 5, 5, 2, 5, 5, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 105 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957762 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957762/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957762 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 34) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCS1) `ZINC000427957762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000427957762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000427957762 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCS1 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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 14, 7, 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] 0 hydrogens 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, 23, 2, 32, 1, 1, 1, 5, 5, 1, 5, 5, 5, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 5, 5, 5, 5, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 103 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957762 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000427957762 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957762/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957762/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000427957762 Building ZINC000174583531 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583531' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583531 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174583531 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583531/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583531 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/35 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/35' -> `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(OC)cc2)C12CCCC2) `ZINC000174583531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174583531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000174583531 none CCO[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)C12CCCC2 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', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 27, 27, 27, 27, 5, 21, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 6, 3, 3, 27, 27, 27, 27, 27, 46, 46, 46, 46, 46, 27, 27, 4, 3, 3, 6, 6, 6, 3, 3, 27, 27, 27, 27, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583531 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583531/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583531 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/36 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/36' -> `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(OC)cc2)C12CCCC2) `ZINC000174583531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174583531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000174583531 none CCO[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)C12CCCC2 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', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 27, 27, 27, 27, 5, 20, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 6, 3, 3, 27, 27, 27, 27, 27, 45, 45, 45, 45, 45, 27, 27, 4, 3, 3, 6, 6, 6, 3, 3, 27, 27, 27, 27, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583531 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174583531 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583531/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583531/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583531 Building ZINC000174583531 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583531' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583531 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174583531 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583531/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583531 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 35) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCO[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)C12CCCC2) `ZINC000174583531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174583531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000174583531 none CCO[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)C12CCCC2 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', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 27, 27, 27, 27, 5, 21, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 6, 3, 3, 27, 27, 27, 27, 27, 46, 46, 46, 46, 46, 27, 27, 4, 3, 3, 6, 6, 6, 3, 3, 27, 27, 27, 27, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583531 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583531/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583531 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 36) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCO[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)C12CCCC2) `ZINC000174583531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174583531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000174583531 none CCO[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)C12CCCC2 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', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 27, 27, 27, 27, 5, 20, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 6, 3, 3, 27, 27, 27, 27, 27, 45, 45, 45, 45, 45, 27, 27, 4, 3, 3, 6, 6, 6, 3, 3, 27, 27, 27, 27, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583531 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174583531 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583531/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583531/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583531 Building ZINC000174583542 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583542' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583542 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174583542 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583542/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583542 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/37 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/37' -> `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(OC)cc2)C12CCCC2) `ZINC000174583542.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174583542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000174583542 none CCO[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)C12CCCC2 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', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 42, 29, 29, 29, 29, 5, 20, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 5, 3, 3, 21, 29, 29, 29, 29, 45, 45, 45, 45, 45, 29, 29, 3, 3, 3, 5, 5, 5, 3, 3, 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, 48]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583542 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583542/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583542 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/38 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/38' -> `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(OC)cc2)C12CCCC2) `ZINC000174583542.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174583542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000174583542 none CCO[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)C12CCCC2 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', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 40, 28, 28, 28, 28, 6, 22, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 6, 3, 3, 23, 28, 28, 28, 28, 41, 41, 41, 41, 41, 28, 28, 3, 3, 3, 6, 6, 6, 3, 3, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583542 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174583542 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583542/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583542/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583542 Building ZINC000174583542 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583542' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583542 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174583542 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583542/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583542 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 37) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCO[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)C12CCCC2) `ZINC000174583542.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174583542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000174583542 none CCO[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)C12CCCC2 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', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 42, 29, 29, 29, 29, 5, 20, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 5, 3, 3, 21, 29, 29, 29, 29, 45, 45, 45, 45, 45, 29, 29, 3, 3, 3, 5, 5, 5, 3, 3, 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, 48]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583542 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583542/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583542 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 38) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCO[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)C12CCCC2) `ZINC000174583542.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174583542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000174583542 none CCO[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)C12CCCC2 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', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 40, 28, 28, 28, 28, 6, 22, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 6, 3, 3, 23, 28, 28, 28, 28, 41, 41, 41, 41, 41, 28, 28, 3, 3, 3, 6, 6, 6, 3, 3, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583542 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174583542 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583542/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583542/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583542 Building ZINC000174583554 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583554' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583554 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174583554 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583554/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583554 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/39 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/39' -> `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(OC)cc2)C12CCCC2) `ZINC000174583554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174583554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000174583554 none CCO[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)C12CCCC2 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', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 40, 28, 28, 28, 23, 6, 22, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 6, 3, 3, 28, 28, 28, 28, 28, 41, 41, 41, 41, 41, 28, 28, 3, 3, 3, 6, 6, 6, 3, 3, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583554 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583554/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583554 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/40 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/40' -> `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(OC)cc2)C12CCCC2) `ZINC000174583554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174583554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000174583554 none CCO[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)C12CCCC2 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', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 31, 31, 31, 23, 5, 21, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 5, 3, 3, 31, 31, 31, 31, 31, 45, 45, 45, 45, 45, 31, 31, 3, 3, 3, 5, 5, 5, 3, 3, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583554 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174583554 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583554/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583554/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583554 Building ZINC000174583554 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583554' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583554 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174583554 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583554/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583554 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 39) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCO[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)C12CCCC2) `ZINC000174583554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174583554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000174583554 none CCO[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)C12CCCC2 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', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 40, 28, 28, 28, 23, 6, 22, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 6, 3, 3, 28, 28, 28, 28, 28, 41, 41, 41, 41, 41, 28, 28, 3, 3, 3, 6, 6, 6, 3, 3, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583554 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583554/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583554 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 40) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCO[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)C12CCCC2) `ZINC000174583554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174583554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000174583554 none CCO[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)C12CCCC2 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', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 31, 31, 31, 23, 5, 21, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 5, 3, 3, 31, 31, 31, 31, 31, 45, 45, 45, 45, 45, 31, 31, 3, 3, 3, 5, 5, 5, 3, 3, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583554 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174583554 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583554/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583554/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583554 Building ZINC000174583565 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583565' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583565 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174583565 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583565/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583565 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/41 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/41' -> `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(OC)cc2)C12CCCC2) `ZINC000174583565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174583565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000174583565 none CCO[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)C12CCCC2 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', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 30, 30, 30, 27, 4, 20, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 6, 3, 3, 30, 30, 30, 30, 30, 45, 45, 45, 45, 45, 30, 30, 3, 3, 3, 6, 6, 6, 3, 3, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583565 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583565/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583565 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/42 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/42' -> `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(OC)cc2)C12CCCC2) `ZINC000174583565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174583565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000174583565 none CCO[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)C12CCCC2 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', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 29, 29, 29, 25, 4, 21, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 6, 3, 3, 29, 29, 29, 29, 29, 46, 46, 46, 46, 46, 29, 29, 3, 3, 3, 6, 6, 6, 3, 3, 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, 48]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583565 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174583565 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583565/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583565/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583565 Building ZINC000174583565 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583565' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583565 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174583565 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583565/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583565 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 41) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCO[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)C12CCCC2) `ZINC000174583565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174583565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000174583565 none CCO[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)C12CCCC2 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', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 30, 30, 30, 27, 4, 20, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 6, 3, 3, 30, 30, 30, 30, 30, 45, 45, 45, 45, 45, 30, 30, 3, 3, 3, 6, 6, 6, 3, 3, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583565 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583565/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583565 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 42) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCO[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)C12CCCC2) `ZINC000174583565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174583565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000174583565 none CCO[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)C12CCCC2 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', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 29, 29, 29, 25, 4, 21, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 6, 3, 3, 29, 29, 29, 29, 29, 46, 46, 46, 46, 46, 29, 29, 3, 3, 3, 6, 6, 6, 3, 3, 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, 48]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583565 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174583565 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583565/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583565/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174583565 Building ZINC000174587689 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587689' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587689 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174587689 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587689/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587689 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/43 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc2ccccc2OC)cc1) `ZINC000174587689.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174587689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000174587689 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 8, 8, 8, 18, 39, 39, 29, 39, 39, 39, 50, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 8, 8, 8, 18, 18, 39, 39, 39, 39, 50, 50, 50, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 196 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587689 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587689/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587689 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/44 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/44' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc2ccccc2OC)cc1) `ZINC000174587689.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174587689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000174587689 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 5, 5, 9, 9, 9, 18, 39, 39, 27, 39, 39, 39, 50, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 9, 9, 9, 18, 18, 39, 39, 39, 39, 50, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587689 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174587689 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587689/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587689/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587689 Building ZINC000174587689 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587689' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587689 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174587689 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587689/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587689 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 43) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc2ccccc2OC)cc1) `ZINC000174587689.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174587689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000174587689 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 8, 8, 8, 18, 39, 39, 29, 39, 39, 39, 50, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 8, 8, 8, 18, 18, 39, 39, 39, 39, 50, 50, 50, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 196 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587689 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587689/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587689 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 44) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc2ccccc2OC)cc1) `ZINC000174587689.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174587689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000174587689 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 5, 5, 9, 9, 9, 18, 39, 39, 27, 39, 39, 39, 50, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 9, 9, 9, 18, 18, 39, 39, 39, 39, 50, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587689 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174587689 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587689/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587689/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587689 Building ZINC000174587675 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587675' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174587675 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587675/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/45 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc2ccccc2OC)cc1) `ZINC000174587675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174587675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000174587675 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 5, 5, 9, 9, 9, 18, 39, 39, 27, 39, 39, 39, 50, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 9, 9, 9, 18, 18, 39, 39, 39, 39, 50, 50, 50, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587675/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/46 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/46' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc2ccccc2OC)cc1) `ZINC000174587675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174587675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000174587675 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 9, 9, 9, 19, 40, 40, 29, 40, 40, 40, 50, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 19, 19, 40, 40, 40, 40, 50, 50, 50, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 200 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174587675 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587675/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587675/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587675 Building ZINC000174587675 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587675' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174587675 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587675/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 45) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc2ccccc2OC)cc1) `ZINC000174587675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174587675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000174587675 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 5, 5, 9, 9, 9, 18, 39, 39, 27, 39, 39, 39, 50, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 9, 9, 9, 18, 18, 39, 39, 39, 39, 50, 50, 50, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587675/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 46) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc2ccccc2OC)cc1) `ZINC000174587675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174587675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000174587675 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 9, 9, 9, 19, 40, 40, 29, 40, 40, 40, 50, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 19, 19, 40, 40, 40, 40, 50, 50, 50, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 200 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174587675 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587675/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587675/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174587675 Building ZINC000108881637 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881637' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881637 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000108881637 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881637/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881637 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/47 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCOc3ccccc32)cc1) `ZINC000108881637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108881637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000108881637 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCOc3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 17, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 3, 17, 17, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6] 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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881637 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881637/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881637 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/48 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/48' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCOc3ccccc32)cc1) `ZINC000108881637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108881637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000108881637 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCOc3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 16, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6, 6, 3, 16, 16, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6] 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]) total number of confs: 150 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881637 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000108881637 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881637/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881637/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881637 Building ZINC000108881637 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881637' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881637 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000108881637 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881637/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881637 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 47) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCOc3ccccc32)cc1) `ZINC000108881637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108881637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000108881637 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCOc3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 17, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 3, 17, 17, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6] 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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881637 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881637/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881637 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 48) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCOc3ccccc32)cc1) `ZINC000108881637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108881637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000108881637 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCOc3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 16, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6, 6, 3, 16, 16, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6] 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]) total number of confs: 150 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881637 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000108881637 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881637/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881637/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881637 Building ZINC000108881639 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881639' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881639 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000108881639 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881639/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881639 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/49 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCOc3ccccc32)cc1) `ZINC000108881639.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108881639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000108881639 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCOc3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 16, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6, 6, 3, 16, 16, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 152 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881639 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881639/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881639 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/50 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/50' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCOc3ccccc32)cc1) `ZINC000108881639.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108881639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881639/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000108881639 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCOc3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 18, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 3, 18, 18, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881639 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000108881639 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881639/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881639/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881639 Building ZINC000108881639 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881639' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881639 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000108881639 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881639/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881639 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 49) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCOc3ccccc32)cc1) `ZINC000108881639.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108881639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000108881639 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCOc3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 16, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6, 6, 3, 16, 16, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 152 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881639 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881639/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881639 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 50) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCOc3ccccc32)cc1) `ZINC000108881639.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108881639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881639/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000108881639 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCOc3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 18, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 3, 18, 18, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881639 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000108881639 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881639/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881639/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000108881639 Building ZINC000621125514 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000621125514' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000621125514 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000621125514 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000621125514/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000621125514 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/51 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@](C)(C(F)F)C1) `ZINC000621125514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000621125514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000621125514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000621125514 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@](C)(C(F)F)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 8, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 10, 8, 8] 11 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: 33 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000621125514 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000621125514/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000621125514 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/52 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/52' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@](C)(C(F)F)C1) `ZINC000621125514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000621125514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000621125514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000621125514 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@](C)(C(F)F)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 6, 7, 13, 13, 13, 13, 13, 13, 13, 13, 22, 22, 13, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 22, 13, 13] 23 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: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000621125514 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000621125514 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000621125514/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000621125514/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000621125514 Building ZINC000621125514 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000621125514' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000621125514 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000621125514 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000621125514/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000621125514 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 51) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@](C)(C(F)F)C1) `ZINC000621125514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000621125514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000621125514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000621125514 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@](C)(C(F)F)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 8, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 10, 8, 8] 11 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: 33 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000621125514 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000621125514/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000621125514 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 52) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@](C)(C(F)F)C1) `ZINC000621125514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000621125514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000621125514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000621125514 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@](C)(C(F)F)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 6, 7, 13, 13, 13, 13, 13, 13, 13, 13, 22, 22, 13, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 22, 13, 13] 23 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: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000621125514 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000621125514 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000621125514/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000621125514/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000621125514 Building ZINC000337103287 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337103287' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337103287 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337103287 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337103287/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337103287 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/53 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCC2=O)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000337103287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337103287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337103287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000337103287 none O=C(Nc1ccc(N2CCC2=O)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', '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, 1, 1, 1, 1, 8, 5, 5, 1, 11, 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, 7, 7, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 7, 7, 33, 33, 33, 33, 15, 15, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 6, 15, 15, 33, 33, 33, 33, 15, 15, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337103287 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337103287/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337103287 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/54 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/54' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCC2=O)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000337103287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337103287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337103287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000337103287 none O=C(Nc1ccc(N2CCC2=O)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', '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, 1, 1, 1, 1, 8, 5, 5, 1, 11, 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, 7, 7, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 20, 20, 7, 11, 34, 33, 34, 34, 20, 20, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 6, 20, 20, 34, 34, 34, 34, 20, 20, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337103287 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337103287 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337103287/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337103287/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337103287 Building ZINC000337103287 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337103287' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337103287 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337103287 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337103287/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337103287 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 53) grep: /scratch/xiaobo/83235/xao-8058115.15/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(Nc1ccc(N2CCC2=O)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000337103287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337103287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337103287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000337103287 none O=C(Nc1ccc(N2CCC2=O)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', '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, 1, 1, 1, 1, 8, 5, 5, 1, 11, 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, 7, 7, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 7, 7, 33, 33, 33, 33, 15, 15, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 6, 15, 15, 33, 33, 33, 33, 15, 15, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337103287 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337103287/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337103287 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 54) grep: /scratch/xiaobo/83235/xao-8058115.15/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(Nc1ccc(N2CCC2=O)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000337103287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337103287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337103287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000337103287 none O=C(Nc1ccc(N2CCC2=O)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', '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, 1, 1, 1, 1, 8, 5, 5, 1, 11, 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, 7, 7, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 20, 20, 7, 11, 34, 33, 34, 34, 20, 20, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 6, 20, 20, 34, 34, 34, 34, 20, 20, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337103287 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337103287 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337103287/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337103287/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337103287 Building ZINC000337111082 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337111082' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337111082 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337111082 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337111082/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337111082 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/55 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N2CCC2=O)cc1) `ZINC000337111082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337111082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337111082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000337111082 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N2CCC2=O)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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 1, 11, 1, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 8, 8, 8, 21, 21, 9, 14, 49, 49, 49, 49, 21, 21, 6, 6, 6, 6, 6, 6, 8, 21, 21, 49, 49, 49, 49, 21, 21] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337111082 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337111082/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337111082 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/56 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/56' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(N2CCC2=O)cc1) `ZINC000337111082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337111082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337111082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000337111082 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(N2CCC2=O)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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 1, 11, 1, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 22, 22, 9, 9, 50, 50, 50, 50, 22, 22, 5, 5, 5, 5, 5, 5, 9, 22, 22, 50, 50, 50, 50, 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]) total number of confs: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337111082 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337111082 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337111082/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337111082/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337111082 Building ZINC000337111082 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337111082' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337111082 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337111082 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337111082/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337111082 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 55) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N2CCC2=O)cc1) `ZINC000337111082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337111082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337111082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000337111082 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N2CCC2=O)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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 1, 11, 1, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 8, 8, 8, 21, 21, 9, 14, 49, 49, 49, 49, 21, 21, 6, 6, 6, 6, 6, 6, 8, 21, 21, 49, 49, 49, 49, 21, 21] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337111082 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337111082/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337111082 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 56) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(N2CCC2=O)cc1) `ZINC000337111082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337111082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337111082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000337111082 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(N2CCC2=O)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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 1, 11, 1, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 22, 22, 9, 9, 50, 50, 50, 50, 22, 22, 5, 5, 5, 5, 5, 5, 9, 22, 22, 50, 50, 50, 50, 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]) total number of confs: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337111082 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337111082 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337111082/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337111082/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337111082 Building ZINC000428206381 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000428206381 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/57 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428206381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428206381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000428206381 none O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 16, 16, 16, 16, 16, 39, 39, 39, 39, 39, 16, 16, 1, 1, 1, 5, 5, 5, 5, 5, 3, 16, 16, 16, 16, 39, 39, 39, 39, 16, 16, 16, 16, 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: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/58 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/58' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428206381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428206381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000428206381 none O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 16, 16, 16, 16, 16, 39, 39, 39, 39, 39, 16, 16, 1, 1, 1, 5, 5, 5, 5, 5, 3, 16, 16, 16, 16, 39, 39, 39, 39, 16, 16, 16, 16, 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: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/59 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/59' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428206381.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000428206381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000428206381 none O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 15, 15, 15, 15, 15, 40, 40, 40, 40, 40, 15, 15, 1, 1, 1, 6, 6, 6, 6, 6, 3, 15, 15, 15, 15, 40, 40, 40, 40, 15, 15, 15, 15, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/60 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/60' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428206381.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000428206381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000428206381 none O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 15, 15, 15, 15, 15, 40, 40, 40, 40, 40, 15, 15, 1, 1, 1, 6, 6, 6, 6, 6, 3, 15, 15, 15, 15, 40, 40, 40, 40, 15, 15, 15, 15, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428206381 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 Building ZINC000428206381 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000428206381 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 57) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428206381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428206381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000428206381 none O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 16, 16, 16, 16, 16, 39, 39, 39, 39, 39, 16, 16, 1, 1, 1, 5, 5, 5, 5, 5, 3, 16, 16, 16, 16, 39, 39, 39, 39, 16, 16, 16, 16, 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: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 58) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428206381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428206381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000428206381 none O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 16, 16, 16, 16, 16, 39, 39, 39, 39, 39, 16, 16, 1, 1, 1, 5, 5, 5, 5, 5, 3, 16, 16, 16, 16, 39, 39, 39, 39, 16, 16, 16, 16, 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: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 59) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428206381.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000428206381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000428206381 none O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 15, 15, 15, 15, 15, 40, 40, 40, 40, 40, 15, 15, 1, 1, 1, 6, 6, 6, 6, 6, 3, 15, 15, 15, 15, 40, 40, 40, 40, 15, 15, 15, 15, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 60) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428206381.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000428206381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000428206381 none O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 15, 15, 15, 15, 15, 40, 40, 40, 40, 40, 15, 15, 1, 1, 1, 6, 6, 6, 6, 6, 3, 15, 15, 15, 15, 40, 40, 40, 40, 15, 15, 15, 15, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428206381 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 Building ZINC000428206381 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000428206381 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 57) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428206381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428206381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000428206381 none O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 16, 16, 16, 16, 16, 39, 39, 39, 39, 39, 16, 16, 1, 1, 1, 5, 5, 5, 5, 5, 3, 16, 16, 16, 16, 39, 39, 39, 39, 16, 16, 16, 16, 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: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 58) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428206381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428206381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000428206381 none O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 16, 16, 16, 16, 16, 39, 39, 39, 39, 39, 16, 16, 1, 1, 1, 5, 5, 5, 5, 5, 3, 16, 16, 16, 16, 39, 39, 39, 39, 16, 16, 16, 16, 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: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 59) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428206381.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000428206381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000428206381 none O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 15, 15, 15, 15, 15, 40, 40, 40, 40, 40, 15, 15, 1, 1, 1, 6, 6, 6, 6, 6, 3, 15, 15, 15, 15, 40, 40, 40, 40, 15, 15, 15, 15, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 60) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428206381.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000428206381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000428206381 none O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 15, 15, 15, 15, 15, 40, 40, 40, 40, 40, 15, 15, 1, 1, 1, 6, 6, 6, 6, 6, 3, 15, 15, 15, 15, 40, 40, 40, 40, 15, 15, 15, 15, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428206381 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 Building ZINC000428206381 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000428206381 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 57) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428206381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428206381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000428206381 none O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 16, 16, 16, 16, 16, 39, 39, 39, 39, 39, 16, 16, 1, 1, 1, 5, 5, 5, 5, 5, 3, 16, 16, 16, 16, 39, 39, 39, 39, 16, 16, 16, 16, 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: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 58) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428206381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428206381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000428206381 none O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 16, 16, 16, 16, 16, 39, 39, 39, 39, 39, 16, 16, 1, 1, 1, 5, 5, 5, 5, 5, 3, 16, 16, 16, 16, 39, 39, 39, 39, 16, 16, 16, 16, 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: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 59) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428206381.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000428206381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000428206381 none O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 15, 15, 15, 15, 15, 40, 40, 40, 40, 40, 15, 15, 1, 1, 1, 6, 6, 6, 6, 6, 3, 15, 15, 15, 15, 40, 40, 40, 40, 15, 15, 15, 15, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 60) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428206381.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000428206381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000428206381 none O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 15, 15, 15, 15, 15, 40, 40, 40, 40, 40, 15, 15, 1, 1, 1, 6, 6, 6, 6, 6, 3, 15, 15, 15, 15, 40, 40, 40, 40, 15, 15, 15, 15, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428206381 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428206381 Building ZINC000337118631 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337118631' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337118631 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337118631 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337118631/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337118631 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/61 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCC2=O)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000337118631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337118631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337118631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000337118631 none O=C(Nc1ccc(N2CCC2=O)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 18, 18, 12, 12, 35, 35, 35, 35, 18, 18, 1, 1, 1, 10, 10, 10, 10, 10, 6, 18, 18, 35, 35, 35, 35, 18, 18, 10, 10] 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: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337118631 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337118631/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337118631 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/62 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/62' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCC2=O)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000337118631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337118631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337118631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000337118631 none O=C(Nc1ccc(N2CCC2=O)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 11, 11, 38, 38, 38, 38, 17, 17, 1, 1, 1, 9, 9, 9, 9, 9, 6, 17, 17, 38, 38, 38, 38, 17, 17, 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337118631 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337118631 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337118631/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337118631/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337118631 Building ZINC000337118631 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337118631' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337118631 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337118631 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337118631/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337118631 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 61) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(Nc1ccc(N2CCC2=O)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000337118631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337118631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337118631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000337118631 none O=C(Nc1ccc(N2CCC2=O)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 18, 18, 12, 12, 35, 35, 35, 35, 18, 18, 1, 1, 1, 10, 10, 10, 10, 10, 6, 18, 18, 35, 35, 35, 35, 18, 18, 10, 10] 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: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337118631 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337118631/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337118631 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 62) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(Nc1ccc(N2CCC2=O)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000337118631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337118631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337118631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000337118631 none O=C(Nc1ccc(N2CCC2=O)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 11, 11, 38, 38, 38, 38, 17, 17, 1, 1, 1, 9, 9, 9, 9, 9, 6, 17, 17, 38, 38, 38, 38, 17, 17, 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337118631 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337118631 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337118631/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337118631/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337118631 Building ZINC000428266644 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428266644' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428266644 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428266644 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428266644/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428266644 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/63 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(c1)OCC(=O)N2)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428266644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428266644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428266644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428266644 none O=C(Nc1ccc2c(c1)OCC(=O)N2)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', '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: [11, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 12, 12, 12, 12, 12, 7, 34, 34, 34, 34, 34, 34, 12, 12] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428266644 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428266644/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428266644 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/64 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/64' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(c1)OCC(=O)N2)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428266644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428266644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428266644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428266644 none O=C(Nc1ccc2c(c1)OCC(=O)N2)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', '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: [11, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 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, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 12, 12, 12, 12, 12, 6, 35, 35, 35, 35, 35, 35, 12, 12] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428266644 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428266644 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428266644/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428266644/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428266644 Building ZINC000428266644 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428266644' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428266644 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428266644 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428266644/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428266644 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 63) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/63: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(c1)OCC(=O)N2)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428266644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428266644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428266644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428266644 none O=C(Nc1ccc2c(c1)OCC(=O)N2)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', '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: [11, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 12, 12, 12, 12, 12, 7, 34, 34, 34, 34, 34, 34, 12, 12] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428266644 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428266644/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428266644 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 64) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/64: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(c1)OCC(=O)N2)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428266644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428266644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428266644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428266644 none O=C(Nc1ccc2c(c1)OCC(=O)N2)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', '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: [11, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 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, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 12, 12, 12, 12, 12, 6, 35, 35, 35, 35, 35, 35, 12, 12] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428266644 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428266644 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428266644/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428266644/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428266644 Building ZINC000428318458 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428318458' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428318458 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428318458 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428318458/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428318458 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/65 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428318458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428318458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428318458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428318458 none O=C(N1CCN(c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 12, 19, 19, 19, 19, 32, 32, 31, 32, 32, 19, 19, 1, 1, 1, 5, 5, 5, 5, 5, 19, 19, 19, 19, 32, 32, 32, 32, 32, 19, 19, 19, 19, 5, 5] 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428318458 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428318458/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428318458 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/66 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/66' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428318458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428318458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428318458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428318458 none O=C(N1CCN(c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 12, 19, 19, 19, 19, 31, 31, 30, 31, 31, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 19, 19, 19, 19, 31, 31, 31, 31, 31, 19, 19, 19, 19, 6, 6] 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428318458 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428318458 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428318458/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428318458/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428318458 Building ZINC000428318458 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428318458' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428318458 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428318458 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428318458/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428318458 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 65) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCN(c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428318458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428318458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428318458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428318458 none O=C(N1CCN(c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 12, 19, 19, 19, 19, 32, 32, 31, 32, 32, 19, 19, 1, 1, 1, 5, 5, 5, 5, 5, 19, 19, 19, 19, 32, 32, 32, 32, 32, 19, 19, 19, 19, 5, 5] 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428318458 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428318458/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428318458 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 66) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCN(c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428318458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428318458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428318458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428318458 none O=C(N1CCN(c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 12, 19, 19, 19, 19, 31, 31, 30, 31, 31, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 19, 19, 19, 19, 31, 31, 31, 31, 31, 19, 19, 19, 19, 6, 6] 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428318458 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428318458 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428318458/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428318458/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428318458 Building ZINC000428451265 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428451265' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428451265 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428451265 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428451265/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428451265 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/67 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2ccc(F)cc2C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000428451265.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428451265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428451265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428451265 none O=C(N1CCOc2ccc(F)cc2C1)[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', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 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, 7] 0 hydrogens 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, 19, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428451265 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428451265/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428451265 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/68 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/68' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2ccc(F)cc2C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000428451265.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428451265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428451265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428451265 none O=C(N1CCOc2ccc(F)cc2C1)[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', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 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, 7] 0 hydrogens 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, 1, 21, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428451265 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428451265 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428451265/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428451265/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428451265 Building ZINC000428451265 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428451265' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428451265 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428451265 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428451265/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428451265 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 67) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCOc2ccc(F)cc2C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000428451265.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428451265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428451265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428451265 none O=C(N1CCOc2ccc(F)cc2C1)[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', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 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, 7] 0 hydrogens 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, 19, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428451265 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428451265/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428451265 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 68) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCOc2ccc(F)cc2C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000428451265.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428451265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428451265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428451265 none O=C(N1CCOc2ccc(F)cc2C1)[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', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 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, 7] 0 hydrogens 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, 1, 21, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428451265 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428451265 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428451265/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428451265/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428451265 Building ZINC001119818328 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119818328' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119818328 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119818328 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119818328/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119818328 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/69 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(N3CCCCC3)nc2)c1) `ZINC001119818328.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119818328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119818328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001119818328 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(N3CCCCC3)nc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 6, 16, 16, 16, 16, 29, 29, 29, 29, 29, 16, 16, 2, 2, 2, 2, 2, 2, 2, 1, 6, 6, 16, 16, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 16, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119818328 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119818328/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119818328 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/70 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/70' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NCc2ccc(N3CCCCC3)nc2)c1) `ZINC001119818328.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119818328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119818328/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001119818328 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCc2ccc(N3CCCCC3)nc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 6, 16, 16, 16, 16, 29, 29, 29, 29, 29, 16, 16, 2, 2, 2, 2, 2, 2, 2, 1, 6, 6, 16, 16, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 16, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119818328 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC001119818328 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119818328/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119818328/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119818328 Building ZINC001119818328 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119818328' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119818328 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119818328 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119818328/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119818328 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 69) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(N3CCCCC3)nc2)c1) `ZINC001119818328.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119818328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119818328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001119818328 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(N3CCCCC3)nc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 6, 16, 16, 16, 16, 29, 29, 29, 29, 29, 16, 16, 2, 2, 2, 2, 2, 2, 2, 1, 6, 6, 16, 16, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 16, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119818328 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119818328/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119818328 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 70) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1cccc([C@]([O-])([SiH3])C(=O)NCc2ccc(N3CCCCC3)nc2)c1) `ZINC001119818328.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119818328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119818328/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001119818328 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCc2ccc(N3CCCCC3)nc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 6, 16, 16, 16, 16, 29, 29, 29, 29, 29, 16, 16, 2, 2, 2, 2, 2, 2, 2, 1, 6, 6, 16, 16, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 16, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119818328 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC001119818328 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119818328/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119818328/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119818328 Building ZINC001131850597 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001131850597' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001131850597 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001131850597 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001131850597/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001131850597 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/71 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCCC1) `ZINC001131850597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001131850597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001131850597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001131850597 none CC(C)(C)OC(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 32, 41, 16, 9, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 174 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001131850597 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001131850597/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001131850597 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/72 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/72' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCCC1) `ZINC001131850597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001131850597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001131850597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001131850597 none CC(C)(C)OC(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 32, 41, 18, 9, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 172 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001131850597 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC001131850597 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001131850597/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001131850597/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001131850597 Building ZINC001131850597 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001131850597' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001131850597 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001131850597 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001131850597/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001131850597 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 71) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/71: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCCC1) `ZINC001131850597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001131850597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001131850597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001131850597 none CC(C)(C)OC(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 32, 41, 16, 9, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 174 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001131850597 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001131850597/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001131850597 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 72) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/72: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCCC1) `ZINC001131850597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001131850597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001131850597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001131850597 none CC(C)(C)OC(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 32, 41, 18, 9, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 172 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001131850597 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC001131850597 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001131850597/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001131850597/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001131850597 Building ZINC001119821527 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119821527' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119821527 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119821527 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119821527/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119821527 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/73 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC(NC(=O)OC(C)(C)C)CC2)c1) `ZINC001119821527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119821527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119821527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001119821527 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC(NC(=O)OC(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 10, 18, 18, 28, 28, 28, 28, 5, 5, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 5, 5, 5, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119821527 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119821527/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119821527 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/74 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/74' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC(NC(=O)OC(C)(C)C)CC2)c1) `ZINC001119821527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119821527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119821527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001119821527 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC(NC(=O)OC(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 10, 18, 18, 26, 27, 27, 27, 4, 4, 3, 3, 3, 3, 2, 3, 3, 4, 4, 4, 4, 4, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119821527 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC001119821527 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119821527/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119821527/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119821527 Building ZINC001119821527 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119821527' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119821527 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119821527 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119821527/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119821527 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 73) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC(NC(=O)OC(C)(C)C)CC2)c1) `ZINC001119821527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119821527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119821527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001119821527 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC(NC(=O)OC(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 10, 18, 18, 28, 28, 28, 28, 5, 5, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 5, 5, 5, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119821527 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119821527/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119821527 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 74) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC(NC(=O)OC(C)(C)C)CC2)c1) `ZINC001119821527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119821527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119821527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001119821527 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC(NC(=O)OC(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 10, 18, 18, 26, 27, 27, 27, 4, 4, 3, 3, 3, 3, 2, 3, 3, 4, 4, 4, 4, 4, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119821527 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC001119821527 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119821527/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119821527/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119821527 Building ZINC000127193296 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127193296' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127193296 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000127193296 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127193296/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127193296 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/75 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCC(C)C)nc2)cc1) `ZINC000127193296.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000127193296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127193296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000127193296 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCC(C)C)nc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 22, 42, 46, 49, 8, 8, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 42, 42, 49, 49, 49, 49, 49, 49, 49, 8, 5, 5] 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127193296 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127193296/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127193296 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/76 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/76' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCC(C)C)nc2)cc1) `ZINC000127193296.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000127193296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127193296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000127193296 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCC(C)C)nc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 18, 39, 44, 47, 8, 8, 5, 5, 5, 5, 5, 5, 5, 3, 8, 8, 39, 39, 47, 47, 47, 47, 47, 47, 47, 8, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127193296 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000127193296 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127193296/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127193296/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127193296 Building ZINC000127193296 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127193296' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127193296 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000127193296 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127193296/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127193296 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 75) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCC(C)C)nc2)cc1) `ZINC000127193296.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000127193296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127193296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000127193296 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCC(C)C)nc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 22, 42, 46, 49, 8, 8, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 42, 42, 49, 49, 49, 49, 49, 49, 49, 8, 5, 5] 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127193296 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127193296/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127193296 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 76) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCC(C)C)nc2)cc1) `ZINC000127193296.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000127193296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127193296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000127193296 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCC(C)C)nc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 18, 39, 44, 47, 8, 8, 5, 5, 5, 5, 5, 5, 5, 3, 8, 8, 39, 39, 47, 47, 47, 47, 47, 47, 47, 8, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127193296 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000127193296 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127193296/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127193296/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127193296 Building ZINC000428512758 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000428512758 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/77 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000428512758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428512758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000428512758 none CN(C)C[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.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, 10, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 13, 13, 13, 13, 13, 7, 13, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 13, 13, 32, 32, 32, 32, 32, 32, 32, 32, 13, 13, 13, 13, 4, 8, 8, 13, 13, 13, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/78 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/78' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000428512758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428512758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000428512758 none CN(C)C[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.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, 10, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 13, 13, 13, 13, 13, 7, 13, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 13, 13, 32, 32, 32, 32, 32, 32, 32, 32, 13, 13, 13, 13, 4, 8, 8, 13, 13, 13, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/79 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/79' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000428512758.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000428512758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000428512758 none CN(C)C[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.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, 10, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 15, 15, 15, 15, 15, 7, 15, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 15, 4, 7, 7, 15, 15, 15, 15] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/80 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/80' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000428512758.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000428512758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000428512758 none CN(C)C[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.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, 10, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 15, 15, 15, 15, 15, 7, 15, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 15, 4, 7, 7, 15, 15, 15, 15] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428512758 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 Building ZINC000428512758 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000428512758 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 77) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN(C)C[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000428512758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428512758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000428512758 none CN(C)C[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.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, 10, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 13, 13, 13, 13, 13, 7, 13, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 13, 13, 32, 32, 32, 32, 32, 32, 32, 32, 13, 13, 13, 13, 4, 8, 8, 13, 13, 13, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 78) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN(C)C[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000428512758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428512758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000428512758 none CN(C)C[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.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, 10, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 13, 13, 13, 13, 13, 7, 13, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 13, 13, 32, 32, 32, 32, 32, 32, 32, 32, 13, 13, 13, 13, 4, 8, 8, 13, 13, 13, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 79) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/79: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000428512758.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000428512758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000428512758 none CN(C)C[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.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, 10, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 15, 15, 15, 15, 15, 7, 15, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 15, 4, 7, 7, 15, 15, 15, 15] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 80) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/80: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000428512758.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000428512758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000428512758 none CN(C)C[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.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, 10, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 15, 15, 15, 15, 15, 7, 15, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 15, 4, 7, 7, 15, 15, 15, 15] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428512758 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 Building ZINC000428512758 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000428512758 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 77) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN(C)C[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000428512758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428512758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000428512758 none CN(C)C[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.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, 10, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 13, 13, 13, 13, 13, 7, 13, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 13, 13, 32, 32, 32, 32, 32, 32, 32, 32, 13, 13, 13, 13, 4, 8, 8, 13, 13, 13, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 78) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN(C)C[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000428512758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428512758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000428512758 none CN(C)C[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.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, 10, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 13, 13, 13, 13, 13, 7, 13, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 13, 13, 32, 32, 32, 32, 32, 32, 32, 32, 13, 13, 13, 13, 4, 8, 8, 13, 13, 13, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 79) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/79: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000428512758.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000428512758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000428512758 none CN(C)C[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.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, 10, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 15, 15, 15, 15, 15, 7, 15, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 15, 4, 7, 7, 15, 15, 15, 15] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 80) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/80: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000428512758.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000428512758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000428512758 none CN(C)C[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.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, 10, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 15, 15, 15, 15, 15, 7, 15, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 15, 4, 7, 7, 15, 15, 15, 15] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428512758 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 Building ZINC000428512758 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000428512758 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 77) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN(C)C[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000428512758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428512758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000428512758 none CN(C)C[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.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, 10, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 13, 13, 13, 13, 13, 7, 13, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 13, 13, 32, 32, 32, 32, 32, 32, 32, 32, 13, 13, 13, 13, 4, 8, 8, 13, 13, 13, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 78) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN(C)C[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000428512758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428512758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000428512758 none CN(C)C[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.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, 10, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 13, 13, 13, 13, 13, 7, 13, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 13, 13, 32, 32, 32, 32, 32, 32, 32, 32, 13, 13, 13, 13, 4, 8, 8, 13, 13, 13, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 79) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/79: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000428512758.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000428512758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000428512758 none CN(C)C[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.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, 10, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 15, 15, 15, 15, 15, 7, 15, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 15, 4, 7, 7, 15, 15, 15, 15] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 80) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/80: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000428512758.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000428512758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000428512758 none CN(C)C[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.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, 10, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 15, 15, 15, 15, 15, 7, 15, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 15, 4, 7, 7, 15, 15, 15, 15] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428512758 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428512758 Building ZINC000428518206 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518206' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518206 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428518206 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518206/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518206 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/81 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]([C@@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428518206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428518206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428518206 none O=C(N1CCC[C@@H]([C@@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 7, 12, 12, 12, 12, 12, 14, 31, 31, 31, 31, 31, 12, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 31, 31, 31, 31, 31, 31, 12, 12, 6, 6] 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]) total number of confs: 83 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518206 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518206/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518206 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/82 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/82' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]([C@@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428518206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428518206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428518206 none O=C(N1CCC[C@@H]([C@@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 8, 15, 15, 15, 15, 15, 19, 30, 30, 30, 30, 30, 15, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 15, 15, 15, 15, 30, 30, 30, 30, 30, 30, 15, 15, 7, 7] 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]) total number of confs: 78 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518206 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428518206 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518206/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518206/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518206 Building ZINC000428518206 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518206' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518206 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428518206 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518206/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518206 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 81) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCC[C@@H]([C@@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428518206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428518206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428518206 none O=C(N1CCC[C@@H]([C@@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 7, 12, 12, 12, 12, 12, 14, 31, 31, 31, 31, 31, 12, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 31, 31, 31, 31, 31, 31, 12, 12, 6, 6] 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]) total number of confs: 83 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518206 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518206/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518206 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 82) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCC[C@@H]([C@@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428518206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428518206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428518206 none O=C(N1CCC[C@@H]([C@@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 8, 15, 15, 15, 15, 15, 19, 30, 30, 30, 30, 30, 15, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 15, 15, 15, 15, 30, 30, 30, 30, 30, 30, 15, 15, 7, 7] 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]) total number of confs: 78 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518206 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428518206 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518206/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518206/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518206 Building ZINC000428518207 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518207' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518207 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428518207 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518207/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518207 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/83 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]([C@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428518207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428518207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428518207 none O=C(N1CCC[C@@H]([C@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 7, 12, 12, 12, 12, 12, 16, 34, 34, 34, 34, 34, 12, 1, 1, 1, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 34, 34, 34, 34, 34, 34, 12, 12, 7, 7] 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]) total number of confs: 90 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518207 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518207/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518207 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/84 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/84' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]([C@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428518207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428518207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428518207 none O=C(N1CCC[C@@H]([C@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 8, 15, 15, 15, 15, 15, 18, 31, 31, 31, 31, 31, 15, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 15, 15, 15, 15, 31, 31, 31, 31, 31, 31, 15, 15, 7, 7] 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]) total number of confs: 84 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518207 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428518207 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518207/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518207/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518207 Building ZINC000428518207 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518207' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518207 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428518207 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518207/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518207 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 83) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCC[C@@H]([C@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428518207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428518207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428518207 none O=C(N1CCC[C@@H]([C@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 7, 12, 12, 12, 12, 12, 16, 34, 34, 34, 34, 34, 12, 1, 1, 1, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 34, 34, 34, 34, 34, 34, 12, 12, 7, 7] 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]) total number of confs: 90 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518207 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518207/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518207 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 84) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCC[C@@H]([C@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428518207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428518207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428518207 none O=C(N1CCC[C@@H]([C@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 8, 15, 15, 15, 15, 15, 18, 31, 31, 31, 31, 31, 15, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 15, 15, 15, 15, 31, 31, 31, 31, 31, 31, 15, 15, 7, 7] 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]) total number of confs: 84 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518207 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428518207 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518207/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518207/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518207 Building ZINC000428518208 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518208' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518208 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428518208 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518208/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518208 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/85 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]([C@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428518208.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428518208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428518208 none O=C(N1CCC[C@H]([C@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 16, 16, 16, 16, 16, 20, 32, 32, 32, 32, 32, 16, 1, 1, 1, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 32, 32, 32, 32, 32, 32, 16, 16, 7, 7] 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]) total number of confs: 84 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518208 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518208/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518208 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/86 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/86' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]([C@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428518208.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428518208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428518208 none O=C(N1CCC[C@H]([C@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 7, 12, 12, 12, 12, 12, 14, 32, 32, 32, 32, 32, 12, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 32, 32, 32, 32, 32, 32, 12, 12, 6, 6] 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]) total number of confs: 85 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518208 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428518208 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518208/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518208/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518208 Building ZINC000428518208 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518208' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518208 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428518208 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518208/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518208 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 85) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCC[C@H]([C@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428518208.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428518208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428518208 none O=C(N1CCC[C@H]([C@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 16, 16, 16, 16, 16, 20, 32, 32, 32, 32, 32, 16, 1, 1, 1, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 32, 32, 32, 32, 32, 32, 16, 16, 7, 7] 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]) total number of confs: 84 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518208 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518208/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518208 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 86) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCC[C@H]([C@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428518208.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428518208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428518208 none O=C(N1CCC[C@H]([C@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 7, 12, 12, 12, 12, 12, 14, 32, 32, 32, 32, 32, 12, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 32, 32, 32, 32, 32, 32, 12, 12, 6, 6] 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]) total number of confs: 85 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518208 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428518208 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518208/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518208/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518208 Building ZINC000428518209 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518209' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518209 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428518209 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518209/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518209 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/87 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]([C@@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428518209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428518209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428518209 none O=C(N1CCC[C@H]([C@@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 16, 16, 16, 16, 16, 19, 32, 32, 32, 32, 32, 16, 1, 1, 1, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 32, 32, 32, 32, 32, 32, 16, 16, 7, 7] 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]) total number of confs: 86 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518209 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518209/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518209 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/88 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/88' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]([C@@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428518209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428518209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428518209 none O=C(N1CCC[C@H]([C@@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 7, 12, 12, 12, 12, 12, 16, 33, 33, 33, 33, 33, 12, 1, 1, 1, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 33, 33, 33, 33, 33, 33, 12, 12, 7, 7] 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]) total number of confs: 88 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518209 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428518209 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518209/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518209/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518209 Building ZINC000428518209 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518209' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518209 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428518209 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518209/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518209 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 87) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCC[C@H]([C@@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428518209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428518209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428518209 none O=C(N1CCC[C@H]([C@@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 16, 16, 16, 16, 16, 19, 32, 32, 32, 32, 32, 16, 1, 1, 1, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 32, 32, 32, 32, 32, 32, 16, 16, 7, 7] 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]) total number of confs: 86 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518209 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518209/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518209 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 88) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCC[C@H]([C@@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428518209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428518209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428518209 none O=C(N1CCC[C@H]([C@@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 7, 12, 12, 12, 12, 12, 16, 33, 33, 33, 33, 33, 12, 1, 1, 1, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 33, 33, 33, 33, 33, 33, 12, 12, 7, 7] 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]) total number of confs: 88 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518209 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428518209 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518209/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518209/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428518209 Building ZINC000428525421 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525421' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525421 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428525421 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525421/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525421 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/89 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc([C@@H]2CNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428525421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428525421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000428525421 none O=C(Nc1cccc([C@@H]2CNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 8, 9, 16, 41, 41, 41, 41, 41, 41, 9, 1, 1, 1, 6, 6, 6, 6, 6, 2, 9, 9, 9, 41, 41, 41, 41, 41, 9, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525421 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525421/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525421 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/90 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/90' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc([C@@H]2CNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428525421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428525421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000428525421 none O=C(Nc1cccc([C@@H]2CNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 9, 9, 9, 9, 17, 42, 42, 42, 42, 42, 42, 9, 1, 1, 1, 7, 7, 7, 7, 7, 3, 9, 9, 9, 42, 42, 42, 42, 42, 9, 7, 7] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525421 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428525421 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525421/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525421/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525421 Building ZINC000428525421 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525421' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525421 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428525421 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525421/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525421 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 89) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(Nc1cccc([C@@H]2CNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428525421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428525421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000428525421 none O=C(Nc1cccc([C@@H]2CNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 8, 9, 16, 41, 41, 41, 41, 41, 41, 9, 1, 1, 1, 6, 6, 6, 6, 6, 2, 9, 9, 9, 41, 41, 41, 41, 41, 9, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525421 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525421/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525421 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 90) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(Nc1cccc([C@@H]2CNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428525421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428525421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000428525421 none O=C(Nc1cccc([C@@H]2CNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 9, 9, 9, 9, 17, 42, 42, 42, 42, 42, 42, 9, 1, 1, 1, 7, 7, 7, 7, 7, 3, 9, 9, 9, 42, 42, 42, 42, 42, 9, 7, 7] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525421 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428525421 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525421/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525421/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525421 Building ZINC000428525422 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525422' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525422 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428525422 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525422/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525422 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/91 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc([C@H]2CNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428525422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428525422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000428525422 none O=C(Nc1cccc([C@H]2CNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 10, 10, 3, 10, 18, 42, 42, 42, 42, 42, 42, 10, 1, 1, 1, 7, 7, 7, 7, 7, 3, 10, 10, 3, 42, 42, 42, 42, 42, 10, 7, 7] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525422 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525422/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525422 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/92 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/92' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc([C@H]2CNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428525422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428525422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000428525422 none O=C(Nc1cccc([C@H]2CNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 2, 9, 16, 41, 41, 41, 41, 41, 41, 9, 1, 1, 1, 6, 6, 6, 6, 6, 2, 9, 9, 2, 41, 41, 41, 41, 41, 9, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525422 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428525422 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525422/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525422/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525422 Building ZINC000428525422 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525422' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525422 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428525422 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525422/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525422 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 91) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(Nc1cccc([C@H]2CNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428525422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428525422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000428525422 none O=C(Nc1cccc([C@H]2CNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 10, 10, 3, 10, 18, 42, 42, 42, 42, 42, 42, 10, 1, 1, 1, 7, 7, 7, 7, 7, 3, 10, 10, 3, 42, 42, 42, 42, 42, 10, 7, 7] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525422 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525422/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525422 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 92) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(Nc1cccc([C@H]2CNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428525422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428525422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000428525422 none O=C(Nc1cccc([C@H]2CNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 2, 9, 16, 41, 41, 41, 41, 41, 41, 9, 1, 1, 1, 6, 6, 6, 6, 6, 2, 9, 9, 2, 41, 41, 41, 41, 41, 9, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525422 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428525422 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525422/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525422/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428525422 Building ZINC000127237517 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237517' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237517 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000127237517 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237517/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237517 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/93 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C[C@H](C)O)c2ccccc2)cc1) `ZINC000127237517.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000127237517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000127237517 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C[C@H](C)O)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 14, 26, 25, 34, 39, 39, 39, 26, 32, 32, 26, 32, 32, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 34, 34, 39, 39, 39, 117, 32, 32, 26, 32, 32, 6, 6] 150 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 355 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237517 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237517/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237517 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/94 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/94' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C[C@H](C)O)c2ccccc2)cc1) `ZINC000127237517.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000127237517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237517/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000127237517 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C[C@H](C)O)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 30, 29, 37, 41, 41, 41, 30, 37, 37, 30, 37, 37, 5, 5, 5, 5, 5, 5, 5, 2, 14, 14, 37, 37, 41, 41, 41, 123, 37, 37, 30, 37, 37, 5, 5] 150 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 367 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237517 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000127237517 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237517/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237517/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237517 Building ZINC000127237517 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237517' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237517 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000127237517 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237517/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237517 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 93) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C[C@H](C)O)c2ccccc2)cc1) `ZINC000127237517.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000127237517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000127237517 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C[C@H](C)O)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 14, 26, 25, 34, 39, 39, 39, 26, 32, 32, 26, 32, 32, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 34, 34, 39, 39, 39, 117, 32, 32, 26, 32, 32, 6, 6] 150 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 355 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237517 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237517/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237517 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 94) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C[C@H](C)O)c2ccccc2)cc1) `ZINC000127237517.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000127237517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237517/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000127237517 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C[C@H](C)O)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 30, 29, 37, 41, 41, 41, 30, 37, 37, 30, 37, 37, 5, 5, 5, 5, 5, 5, 5, 2, 14, 14, 37, 37, 41, 41, 41, 123, 37, 37, 30, 37, 37, 5, 5] 150 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 367 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237517 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000127237517 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237517/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237517/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237517 Building ZINC000127237770 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237770' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237770 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000127237770 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237770/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237770 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/95 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C[C@@H](C)O)c2ccccc2)cc1) `ZINC000127237770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000127237770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000127237770 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C[C@@H](C)O)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 11, 22, 22, 25, 35, 35, 35, 22, 27, 27, 22, 27, 27, 6, 6, 6, 6, 6, 6, 6, 3, 11, 11, 25, 25, 35, 35, 35, 105, 27, 27, 22, 27, 27, 6, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 322 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237770 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237770/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237770 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/96 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/96' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C[C@@H](C)O)c2ccccc2)cc1) `ZINC000127237770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000127237770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000127237770 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C[C@@H](C)O)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 25, 25, 26, 34, 34, 34, 25, 31, 31, 25, 31, 31, 6, 6, 6, 6, 6, 6, 6, 3, 15, 15, 26, 26, 34, 34, 34, 102, 31, 31, 25, 31, 31, 6, 6] 150 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 311 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237770 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000127237770 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237770/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237770/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237770 Building ZINC000127237770 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237770' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237770 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000127237770 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237770/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237770 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 95) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C[C@@H](C)O)c2ccccc2)cc1) `ZINC000127237770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000127237770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000127237770 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C[C@@H](C)O)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 11, 22, 22, 25, 35, 35, 35, 22, 27, 27, 22, 27, 27, 6, 6, 6, 6, 6, 6, 6, 3, 11, 11, 25, 25, 35, 35, 35, 105, 27, 27, 22, 27, 27, 6, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 322 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237770 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237770/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237770 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 96) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C[C@@H](C)O)c2ccccc2)cc1) `ZINC000127237770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000127237770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000127237770 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C[C@@H](C)O)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 25, 25, 26, 34, 34, 34, 25, 31, 31, 25, 31, 31, 6, 6, 6, 6, 6, 6, 6, 3, 15, 15, 26, 26, 34, 34, 34, 102, 31, 31, 25, 31, 31, 6, 6] 150 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 311 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237770 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000127237770 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237770/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237770/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127237770 Building ZINC000127238011 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238011' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238011 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000127238011 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238011/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238011 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/97 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C[C@H](C)O)c2ccccc2)cc1) `ZINC000127238011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000127238011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000127238011 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C[C@H](C)O)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 25, 25, 26, 34, 34, 34, 25, 31, 31, 25, 31, 31, 6, 6, 6, 6, 6, 6, 6, 3, 15, 15, 26, 26, 34, 34, 34, 102, 31, 31, 25, 31, 31, 6, 6] 150 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 311 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238011 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238011/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238011 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/98 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/98' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C[C@H](C)O)c2ccccc2)cc1) `ZINC000127238011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000127238011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000127238011 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C[C@H](C)O)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 11, 22, 22, 26, 36, 36, 36, 22, 27, 27, 22, 27, 27, 6, 6, 6, 6, 6, 6, 6, 3, 11, 11, 26, 26, 36, 36, 36, 108, 27, 27, 22, 27, 27, 6, 6] 150 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 330 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238011 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000127238011 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238011/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238011/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238011 Building ZINC000127238011 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238011' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238011 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000127238011 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238011/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238011 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 97) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C[C@H](C)O)c2ccccc2)cc1) `ZINC000127238011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000127238011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000127238011 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C[C@H](C)O)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 25, 25, 26, 34, 34, 34, 25, 31, 31, 25, 31, 31, 6, 6, 6, 6, 6, 6, 6, 3, 15, 15, 26, 26, 34, 34, 34, 102, 31, 31, 25, 31, 31, 6, 6] 150 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 311 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238011 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238011/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238011 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 98) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C[C@H](C)O)c2ccccc2)cc1) `ZINC000127238011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000127238011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000127238011 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C[C@H](C)O)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 11, 22, 22, 26, 36, 36, 36, 22, 27, 27, 22, 27, 27, 6, 6, 6, 6, 6, 6, 6, 3, 11, 11, 26, 26, 36, 36, 36, 108, 27, 27, 22, 27, 27, 6, 6] 150 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 330 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238011 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000127238011 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238011/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238011/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238011 Building ZINC000127238229 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238229' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238229 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000127238229 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238229/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238229 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/99 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C[C@@H](C)O)c2ccccc2)cc1) `ZINC000127238229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000127238229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000127238229 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C[C@@H](C)O)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 2, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 29, 28, 37, 41, 41, 41, 29, 36, 36, 29, 36, 36, 5, 5, 5, 5, 5, 5, 5, 2, 14, 14, 37, 37, 41, 41, 41, 123, 36, 36, 29, 36, 36, 5, 5] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 368 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238229 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238229/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238229 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/100 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/100' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C[C@@H](C)O)c2ccccc2)cc1) `ZINC000127238229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000127238229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000127238229 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C[C@@H](C)O)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 14, 26, 25, 35, 38, 38, 38, 26, 32, 32, 26, 32, 32, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 35, 35, 38, 38, 38, 114, 32, 32, 26, 32, 32, 6, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 342 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238229 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000127238229 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238229/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238229/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238229 Building ZINC000127238229 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238229' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238229 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000127238229 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238229/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238229 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 99) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/99: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C[C@@H](C)O)c2ccccc2)cc1) `ZINC000127238229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000127238229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000127238229 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C[C@@H](C)O)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 2, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 29, 28, 37, 41, 41, 41, 29, 36, 36, 29, 36, 36, 5, 5, 5, 5, 5, 5, 5, 2, 14, 14, 37, 37, 41, 41, 41, 123, 36, 36, 29, 36, 36, 5, 5] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 368 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238229 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238229/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238229 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 100) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/100: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C[C@@H](C)O)c2ccccc2)cc1) `ZINC000127238229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000127238229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000127238229 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C[C@@H](C)O)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 14, 26, 25, 35, 38, 38, 38, 26, 32, 32, 26, 32, 32, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 35, 35, 38, 38, 38, 114, 32, 32, 26, 32, 32, 6, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 342 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238229 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000127238229 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238229/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238229/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000127238229 Building ZINC000428616080 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428616080' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428616080 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428616080 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428616080/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428616080 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/101 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cnc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)s1) `ZINC000428616080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428616080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428616080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000428616080 none CCc1cnc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', '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', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 27, 27, 27, 27, 15, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 27, 43, 43, 43, 43, 43, 27, 15, 15, 10, 10, 2, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428616080 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428616080/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428616080 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/102 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/102' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cnc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)s1) `ZINC000428616080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428616080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428616080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000428616080 none CCc1cnc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', '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', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 26, 26, 26, 26, 15, 10, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 26, 44, 44, 44, 44, 44, 26, 15, 15, 10, 10, 2, 7, 7] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428616080 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428616080 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428616080/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428616080/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428616080 Building ZINC000428616080 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428616080' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428616080 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428616080 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428616080/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428616080 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 101) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCc1cnc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)s1) `ZINC000428616080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428616080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428616080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000428616080 none CCc1cnc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', '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', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 27, 27, 27, 27, 15, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 27, 43, 43, 43, 43, 43, 27, 15, 15, 10, 10, 2, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428616080 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428616080/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428616080 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 102) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCc1cnc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)s1) `ZINC000428616080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428616080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428616080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000428616080 none CCc1cnc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', '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', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 26, 26, 26, 26, 15, 10, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 26, 44, 44, 44, 44, 44, 26, 15, 15, 10, 10, 2, 7, 7] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428616080 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428616080 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428616080/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428616080/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428616080 Building ZINC000428622481 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428622481' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428622481 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428622481 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428622481/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428622481 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/103 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)Cc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428622481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428622481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428622481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428622481 none COC(=O)Cc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 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: [43, 43, 22, 43, 8, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 43, 43, 43, 22, 22, 8, 8, 8, 8, 3, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428622481 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428622481/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428622481 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/104 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/104' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)Cc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428622481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428622481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428622481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428622481 none COC(=O)Cc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 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: [43, 43, 22, 43, 8, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 43, 43, 43, 22, 22, 8, 8, 8, 8, 3, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428622481 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428622481 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428622481/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428622481/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428622481 Building ZINC000428622481 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428622481' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428622481 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428622481 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428622481/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428622481 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 103) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC(=O)Cc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428622481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428622481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428622481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428622481 none COC(=O)Cc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 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: [43, 43, 22, 43, 8, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 43, 43, 43, 22, 22, 8, 8, 8, 8, 3, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428622481 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428622481/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428622481 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 104) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC(=O)Cc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428622481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428622481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428622481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428622481 none COC(=O)Cc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 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: [43, 43, 22, 43, 8, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 43, 43, 43, 22, 22, 8, 8, 8, 8, 3, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428622481 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428622481 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428622481/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428622481/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428622481 Building ZINC000428621459 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428621459' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428621459 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428621459 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428621459/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428621459 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/105 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(C(F)(F)F)CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428621459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428621459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428621459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000428621459 none O=C(NC1(C(F)(F)F)CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 15, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 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 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, 21, 21, 1, 1, 1, 11, 11, 11, 11, 11, 6, 21, 21, 21, 21, 21, 21, 21, 21, 11, 11] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428621459 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428621459/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428621459 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/106 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/106' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(C(F)(F)F)CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428621459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428621459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428621459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000428621459 none O=C(NC1(C(F)(F)F)CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 15, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 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 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, 21, 21, 1, 1, 1, 11, 11, 11, 11, 11, 6, 21, 21, 21, 21, 21, 21, 21, 21, 11, 11] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428621459 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428621459 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428621459/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428621459/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428621459 Building ZINC000428621459 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428621459' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428621459 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428621459 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428621459/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428621459 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 105) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NC1(C(F)(F)F)CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428621459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428621459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428621459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000428621459 none O=C(NC1(C(F)(F)F)CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 15, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 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 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, 21, 21, 1, 1, 1, 11, 11, 11, 11, 11, 6, 21, 21, 21, 21, 21, 21, 21, 21, 11, 11] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428621459 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428621459/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428621459 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 106) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NC1(C(F)(F)F)CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428621459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428621459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428621459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000428621459 none O=C(NC1(C(F)(F)F)CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 15, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 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 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, 21, 21, 1, 1, 1, 11, 11, 11, 11, 11, 6, 21, 21, 21, 21, 21, 21, 21, 21, 11, 11] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428621459 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428621459 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428621459/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428621459/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428621459 Building ZINC000428630334 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630334' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428630334 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630334/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/107 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC000428630334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428630334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000428630334 none COC[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 11, 6, 11, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 29, 29, 29, 27, 27, 11, 11, 11, 6, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630334/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/108 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/108' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@](C)(NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC000428630334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428630334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000428630334 none COC[C@](C)(NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 29, 12, 6, 12, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 12, 12, 12, 12, 34, 34, 34, 29, 29, 12, 12, 12, 6, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428630334 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630334/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630334/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630334 Building ZINC000428630334 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630334' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428630334 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630334/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 107) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC000428630334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428630334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000428630334 none COC[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 11, 6, 11, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 29, 29, 29, 27, 27, 11, 11, 11, 6, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630334/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 108) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC[C@](C)(NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC000428630334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428630334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000428630334 none COC[C@](C)(NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 29, 12, 6, 12, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 12, 12, 12, 12, 34, 34, 34, 29, 29, 12, 12, 12, 6, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428630334 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630334/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630334/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630334 Building ZINC000428630335 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630335' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630335 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428630335 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630335/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630335 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/109 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC000428630335.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428630335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000428630335 none COC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 29, 12, 6, 12, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 12, 12, 12, 12, 34, 34, 34, 29, 29, 12, 12, 12, 6, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630335 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630335/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630335 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/110 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/110' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC000428630335.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428630335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000428630335 none COC[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 11, 6, 11, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 29, 29, 29, 27, 27, 11, 11, 11, 6, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630335 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428630335 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630335/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630335/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630335 Building ZINC000428630335 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630335' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630335 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428630335 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630335/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630335 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 109) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC000428630335.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428630335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000428630335 none COC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 29, 12, 6, 12, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 12, 12, 12, 12, 34, 34, 34, 29, 29, 12, 12, 12, 6, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630335 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630335/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630335 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 110) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC000428630335.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428630335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000428630335 none COC[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 11, 6, 11, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 29, 29, 29, 27, 27, 11, 11, 11, 6, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630335 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428630335 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630335/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630335/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428630335 Building ZINC000428648018 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648018' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648018 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428648018 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648018/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648018 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/111 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428648018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428648018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428648018 none Cc1nn(C)c(C)c1C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [33, 33, 33, 33, 33, 33, 33, 21, 11, 4, 11, 11, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 21, 21, 11, 11, 11, 4, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 117 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648018 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648018/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648018 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/112 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/112' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428648018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428648018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428648018 none Cc1nn(C)c(C)c1C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [32, 32, 32, 32, 32, 32, 32, 22, 10, 3, 10, 10, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 22, 10, 10, 10, 3, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 118 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648018 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428648018 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648018/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648018/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648018 Building ZINC000428648018 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648018' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648018 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428648018 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648018/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648018 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 111) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(C)c1C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428648018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428648018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428648018 none Cc1nn(C)c(C)c1C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [33, 33, 33, 33, 33, 33, 33, 21, 11, 4, 11, 11, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 21, 21, 11, 11, 11, 4, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 117 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648018 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648018/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648018 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 112) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(C)c1C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428648018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428648018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428648018 none Cc1nn(C)c(C)c1C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [32, 32, 32, 32, 32, 32, 32, 22, 10, 3, 10, 10, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 22, 10, 10, 10, 3, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 118 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648018 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428648018 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648018/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648018/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648018 Building ZINC000428648020 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648020' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648020 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428648020 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648020/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648020 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/113 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428648020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428648020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428648020 none Cc1nn(C)c(C)c1C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [32, 32, 32, 32, 32, 32, 32, 22, 11, 3, 11, 11, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 22, 11, 11, 11, 3, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 115 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648020 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648020/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648020 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/114 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/114' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428648020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428648020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428648020 none Cc1nn(C)c(C)c1C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [33, 33, 33, 33, 33, 33, 33, 21, 11, 4, 11, 11, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 21, 21, 11, 11, 11, 4, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 117 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648020 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428648020 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648020/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648020/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648020 Building ZINC000428648020 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648020' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648020 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428648020 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648020/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648020 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 113) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/113: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428648020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428648020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428648020 none Cc1nn(C)c(C)c1C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [32, 32, 32, 32, 32, 32, 32, 22, 11, 3, 11, 11, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 22, 11, 11, 11, 3, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 115 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648020 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648020/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648020 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 114) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/114: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428648020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428648020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428648020 none Cc1nn(C)c(C)c1C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [33, 33, 33, 33, 33, 33, 33, 21, 11, 4, 11, 11, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 21, 21, 11, 11, 11, 4, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 117 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648020 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428648020 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648020/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648020/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428648020 Building ZINC000428650663 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000428650663 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/115 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428650663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650663 none CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 8, 18, 4, 6, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 18, 18, 18, 18, 30, 30, 30, 30, 30, 18, 18, 18, 18, 6, 6, 6, 8, 8, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 126 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/116 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/116' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428650663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650663 none CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 8, 18, 4, 6, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 18, 18, 18, 18, 30, 30, 30, 30, 30, 18, 18, 18, 18, 6, 6, 6, 8, 8, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 126 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/117 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/117' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650663.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000428650663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650663 none CCN1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 6, 19, 3, 4, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 19, 19, 19, 19, 31, 31, 31, 31, 31, 19, 19, 19, 19, 4, 4, 4, 8, 8, 19, 19, 19, 19, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 124 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/118 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/118' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650663.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000428650663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650663 none CCN1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 6, 19, 3, 4, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 19, 19, 19, 19, 31, 31, 31, 31, 31, 19, 19, 19, 19, 4, 4, 4, 8, 8, 19, 19, 19, 19, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 124 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428650663 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 Building ZINC000428650663 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000428650663 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 115) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428650663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650663 none CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 8, 18, 4, 6, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 18, 18, 18, 18, 30, 30, 30, 30, 30, 18, 18, 18, 18, 6, 6, 6, 8, 8, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 126 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 116) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428650663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650663 none CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 8, 18, 4, 6, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 18, 18, 18, 18, 30, 30, 30, 30, 30, 18, 18, 18, 18, 6, 6, 6, 8, 8, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 126 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 117) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/117: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650663.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000428650663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650663 none CCN1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 6, 19, 3, 4, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 19, 19, 19, 19, 31, 31, 31, 31, 31, 19, 19, 19, 19, 4, 4, 4, 8, 8, 19, 19, 19, 19, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 124 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 118) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/118: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650663.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000428650663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650663 none CCN1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 6, 19, 3, 4, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 19, 19, 19, 19, 31, 31, 31, 31, 31, 19, 19, 19, 19, 4, 4, 4, 8, 8, 19, 19, 19, 19, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 124 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428650663 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 Building ZINC000428650663 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000428650663 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 115) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428650663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650663 none CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 8, 18, 4, 6, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 18, 18, 18, 18, 30, 30, 30, 30, 30, 18, 18, 18, 18, 6, 6, 6, 8, 8, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 126 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 116) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428650663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650663 none CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 8, 18, 4, 6, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 18, 18, 18, 18, 30, 30, 30, 30, 30, 18, 18, 18, 18, 6, 6, 6, 8, 8, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 126 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 117) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/117: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650663.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000428650663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650663 none CCN1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 6, 19, 3, 4, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 19, 19, 19, 19, 31, 31, 31, 31, 31, 19, 19, 19, 19, 4, 4, 4, 8, 8, 19, 19, 19, 19, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 124 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 118) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/118: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650663.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000428650663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650663 none CCN1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 6, 19, 3, 4, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 19, 19, 19, 19, 31, 31, 31, 31, 31, 19, 19, 19, 19, 4, 4, 4, 8, 8, 19, 19, 19, 19, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 124 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428650663 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 Building ZINC000428650663 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000428650663 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 115) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428650663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650663 none CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 8, 18, 4, 6, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 18, 18, 18, 18, 30, 30, 30, 30, 30, 18, 18, 18, 18, 6, 6, 6, 8, 8, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 126 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 116) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428650663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650663 none CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 8, 18, 4, 6, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 18, 18, 18, 18, 30, 30, 30, 30, 30, 18, 18, 18, 18, 6, 6, 6, 8, 8, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 126 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 117) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/117: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650663.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000428650663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650663 none CCN1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 6, 19, 3, 4, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 19, 19, 19, 19, 31, 31, 31, 31, 31, 19, 19, 19, 19, 4, 4, 4, 8, 8, 19, 19, 19, 19, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 124 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 118) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/118: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650663.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000428650663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650663 none CCN1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 6, 19, 3, 4, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 19, 19, 19, 19, 31, 31, 31, 31, 31, 19, 19, 19, 19, 4, 4, 4, 8, 8, 19, 19, 19, 19, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 124 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428650663 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650663 Building ZINC000428650664 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000428650664 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/119 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428650664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650664 none CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 8, 16, 5, 7, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 16, 16, 16, 16, 29, 29, 29, 29, 29, 16, 16, 16, 16, 7, 7, 7, 11, 11, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/120 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/120' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428650664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650664 none CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 8, 16, 5, 7, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 16, 16, 16, 16, 29, 29, 29, 29, 29, 16, 16, 16, 16, 7, 7, 7, 11, 11, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/121 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/121' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650664.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000428650664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650664 none CCN1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 8, 12, 5, 7, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 12, 12, 12, 12, 28, 28, 28, 28, 28, 12, 12, 12, 12, 7, 7, 7, 11, 11, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/122 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/122' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650664.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000428650664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650664 none CCN1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 8, 12, 5, 7, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 12, 12, 12, 12, 28, 28, 28, 28, 28, 12, 12, 12, 12, 7, 7, 7, 11, 11, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428650664 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 Building ZINC000428650664 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000428650664 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 119) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428650664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650664 none CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 8, 16, 5, 7, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 16, 16, 16, 16, 29, 29, 29, 29, 29, 16, 16, 16, 16, 7, 7, 7, 11, 11, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 120) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428650664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650664 none CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 8, 16, 5, 7, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 16, 16, 16, 16, 29, 29, 29, 29, 29, 16, 16, 16, 16, 7, 7, 7, 11, 11, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 121) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650664.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000428650664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650664 none CCN1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 8, 12, 5, 7, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 12, 12, 12, 12, 28, 28, 28, 28, 28, 12, 12, 12, 12, 7, 7, 7, 11, 11, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 122) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/122: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650664.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000428650664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650664 none CCN1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 8, 12, 5, 7, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 12, 12, 12, 12, 28, 28, 28, 28, 28, 12, 12, 12, 12, 7, 7, 7, 11, 11, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428650664 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 Building ZINC000428650664 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000428650664 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 119) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428650664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650664 none CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 8, 16, 5, 7, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 16, 16, 16, 16, 29, 29, 29, 29, 29, 16, 16, 16, 16, 7, 7, 7, 11, 11, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 120) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428650664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650664 none CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 8, 16, 5, 7, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 16, 16, 16, 16, 29, 29, 29, 29, 29, 16, 16, 16, 16, 7, 7, 7, 11, 11, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 121) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650664.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000428650664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650664 none CCN1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 8, 12, 5, 7, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 12, 12, 12, 12, 28, 28, 28, 28, 28, 12, 12, 12, 12, 7, 7, 7, 11, 11, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 122) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/122: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650664.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000428650664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650664 none CCN1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 8, 12, 5, 7, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 12, 12, 12, 12, 28, 28, 28, 28, 28, 12, 12, 12, 12, 7, 7, 7, 11, 11, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428650664 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 Building ZINC000428650664 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000428650664 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 119) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428650664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650664 none CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 8, 16, 5, 7, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 16, 16, 16, 16, 29, 29, 29, 29, 29, 16, 16, 16, 16, 7, 7, 7, 11, 11, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 120) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428650664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650664 none CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 8, 16, 5, 7, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 16, 16, 16, 16, 29, 29, 29, 29, 29, 16, 16, 16, 16, 7, 7, 7, 11, 11, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 121) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650664.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000428650664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650664 none CCN1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 8, 12, 5, 7, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 12, 12, 12, 12, 28, 28, 28, 28, 28, 12, 12, 12, 12, 7, 7, 7, 11, 11, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 122) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/122: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1) `ZINC000428650664.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000428650664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650664 none CCN1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 8, 12, 5, 7, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 12, 12, 12, 12, 28, 28, 28, 28, 28, 12, 12, 12, 12, 7, 7, 7, 11, 11, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428650664 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650664 Building ZINC000428650666 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000428650666 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/123 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650666.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428650666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650666 none CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 22, 22, 22, 22, 5, 22, 3, 5, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 22, 22, 22, 22, 32, 32, 32, 32, 32, 22, 22, 22, 22, 5, 5, 5, 7, 7, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/124 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/124' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650666.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428650666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650666 none CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 22, 22, 22, 22, 5, 22, 3, 5, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 22, 22, 22, 22, 32, 32, 32, 32, 32, 22, 22, 22, 22, 5, 5, 5, 7, 7, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/125 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/125' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650666.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000428650666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650666 none CCN1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 6, 18, 4, 6, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 18, 18, 18, 18, 30, 30, 30, 30, 30, 18, 18, 18, 18, 6, 6, 6, 7, 7, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 120 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/126 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/126' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650666.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000428650666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650666 none CCN1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 6, 18, 4, 6, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 18, 18, 18, 18, 30, 30, 30, 30, 30, 18, 18, 18, 18, 6, 6, 6, 7, 7, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 120 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428650666 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 Building ZINC000428650666 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000428650666 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 123) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650666.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428650666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650666 none CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 22, 22, 22, 22, 5, 22, 3, 5, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 22, 22, 22, 22, 32, 32, 32, 32, 32, 22, 22, 22, 22, 5, 5, 5, 7, 7, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 124) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650666.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428650666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650666 none CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 22, 22, 22, 22, 5, 22, 3, 5, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 22, 22, 22, 22, 32, 32, 32, 32, 32, 22, 22, 22, 22, 5, 5, 5, 7, 7, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 125) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650666.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000428650666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650666 none CCN1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 6, 18, 4, 6, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 18, 18, 18, 18, 30, 30, 30, 30, 30, 18, 18, 18, 18, 6, 6, 6, 7, 7, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 120 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 126) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/126: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650666.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000428650666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650666 none CCN1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 6, 18, 4, 6, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 18, 18, 18, 18, 30, 30, 30, 30, 30, 18, 18, 18, 18, 6, 6, 6, 7, 7, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 120 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428650666 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 Building ZINC000428650666 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000428650666 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 123) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650666.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428650666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650666 none CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 22, 22, 22, 22, 5, 22, 3, 5, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 22, 22, 22, 22, 32, 32, 32, 32, 32, 22, 22, 22, 22, 5, 5, 5, 7, 7, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 124) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650666.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428650666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650666 none CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 22, 22, 22, 22, 5, 22, 3, 5, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 22, 22, 22, 22, 32, 32, 32, 32, 32, 22, 22, 22, 22, 5, 5, 5, 7, 7, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 125) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650666.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000428650666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650666 none CCN1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 6, 18, 4, 6, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 18, 18, 18, 18, 30, 30, 30, 30, 30, 18, 18, 18, 18, 6, 6, 6, 7, 7, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 120 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 126) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/126: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650666.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000428650666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650666 none CCN1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 6, 18, 4, 6, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 18, 18, 18, 18, 30, 30, 30, 30, 30, 18, 18, 18, 18, 6, 6, 6, 7, 7, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 120 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428650666 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 Building ZINC000428650666 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000428650666 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 123) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650666.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428650666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650666 none CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 22, 22, 22, 22, 5, 22, 3, 5, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 22, 22, 22, 22, 32, 32, 32, 32, 32, 22, 22, 22, 22, 5, 5, 5, 7, 7, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 124) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650666.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428650666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650666 none CCN1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 22, 22, 22, 22, 5, 22, 3, 5, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 22, 22, 22, 22, 32, 32, 32, 32, 32, 22, 22, 22, 22, 5, 5, 5, 7, 7, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 125) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650666.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000428650666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650666 none CCN1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 6, 18, 4, 6, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 18, 18, 18, 18, 30, 30, 30, 30, 30, 18, 18, 18, 18, 6, 6, 6, 7, 7, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 120 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 126) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/126: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650666.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000428650666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650666 none CCN1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 6, 18, 4, 6, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 18, 18, 18, 18, 30, 30, 30, 30, 30, 18, 18, 18, 18, 6, 6, 6, 7, 7, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 120 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428650666 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650666 Building ZINC000428650667 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000428650667 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/127 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428650667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650667 none CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 8, 12, 5, 7, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 12, 12, 12, 12, 28, 28, 28, 28, 28, 12, 12, 12, 12, 7, 7, 7, 11, 11, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/128 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/128' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428650667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650667 none CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 8, 12, 5, 7, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 12, 12, 12, 12, 28, 28, 28, 28, 28, 12, 12, 12, 12, 7, 7, 7, 11, 11, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/129 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/129' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650667.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000428650667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650667 none CCN1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 8, 16, 5, 7, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 16, 16, 16, 16, 28, 28, 28, 28, 28, 16, 16, 16, 16, 7, 7, 7, 12, 12, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/130 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/130' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650667.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000428650667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650667 none CCN1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 8, 16, 5, 7, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 16, 16, 16, 16, 28, 28, 28, 28, 28, 16, 16, 16, 16, 7, 7, 7, 12, 12, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428650667 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 Building ZINC000428650667 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000428650667 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 127) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428650667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650667 none CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 8, 12, 5, 7, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 12, 12, 12, 12, 28, 28, 28, 28, 28, 12, 12, 12, 12, 7, 7, 7, 11, 11, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 128) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428650667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650667 none CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 8, 12, 5, 7, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 12, 12, 12, 12, 28, 28, 28, 28, 28, 12, 12, 12, 12, 7, 7, 7, 11, 11, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 129) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/129: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650667.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000428650667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650667 none CCN1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 8, 16, 5, 7, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 16, 16, 16, 16, 28, 28, 28, 28, 28, 16, 16, 16, 16, 7, 7, 7, 12, 12, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 130) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/130: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650667.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000428650667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650667 none CCN1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 8, 16, 5, 7, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 16, 16, 16, 16, 28, 28, 28, 28, 28, 16, 16, 16, 16, 7, 7, 7, 12, 12, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428650667 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 Building ZINC000428650667 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000428650667 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 127) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428650667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650667 none CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 8, 12, 5, 7, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 12, 12, 12, 12, 28, 28, 28, 28, 28, 12, 12, 12, 12, 7, 7, 7, 11, 11, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 128) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428650667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650667 none CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 8, 12, 5, 7, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 12, 12, 12, 12, 28, 28, 28, 28, 28, 12, 12, 12, 12, 7, 7, 7, 11, 11, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 129) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/129: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650667.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000428650667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650667 none CCN1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 8, 16, 5, 7, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 16, 16, 16, 16, 28, 28, 28, 28, 28, 16, 16, 16, 16, 7, 7, 7, 12, 12, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 130) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/130: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650667.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000428650667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650667 none CCN1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 8, 16, 5, 7, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 16, 16, 16, 16, 28, 28, 28, 28, 28, 16, 16, 16, 16, 7, 7, 7, 12, 12, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428650667 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 Building ZINC000428650667 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000428650667 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 127) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428650667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650667 none CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 8, 12, 5, 7, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 12, 12, 12, 12, 28, 28, 28, 28, 28, 12, 12, 12, 12, 7, 7, 7, 11, 11, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 128) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428650667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650667 none CCN1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 8, 12, 5, 7, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 12, 12, 12, 12, 28, 28, 28, 28, 28, 12, 12, 12, 12, 7, 7, 7, 11, 11, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 129) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/129: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650667.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000428650667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650667 none CCN1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 8, 16, 5, 7, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 16, 16, 16, 16, 28, 28, 28, 28, 28, 16, 16, 16, 16, 7, 7, 7, 12, 12, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 130) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/130: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1) `ZINC000428650667.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000428650667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000428650667 none CCN1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 8, 16, 5, 7, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 16, 16, 16, 16, 28, 28, 28, 28, 28, 16, 16, 16, 16, 7, 7, 7, 12, 12, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428650667 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428650667 Building ZINC001119839070 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119839070' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119839070 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119839070 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119839070/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119839070 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/131 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCCN(C)C)cc2)c1) `ZINC001119839070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119839070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119839070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001119839070 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCCN(C)C)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 20, 26, 26, 32, 32, 4, 4, 4, 4, 4, 4, 2, 4, 4, 2, 4, 4, 26, 26, 26, 26, 32, 32, 32, 32, 32, 32, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119839070 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119839070/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119839070 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/132 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/132' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCCN(C)C)cc2)c1) `ZINC001119839070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119839070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119839070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001119839070 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCCN(C)C)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 21, 26, 26, 32, 32, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 26, 26, 26, 26, 32, 32, 32, 32, 32, 32, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119839070 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC001119839070 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119839070/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119839070/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119839070 Building ZINC001119839070 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119839070' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119839070 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119839070 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119839070/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119839070 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 131) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCCN(C)C)cc2)c1) `ZINC001119839070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119839070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119839070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001119839070 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCCN(C)C)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 20, 26, 26, 32, 32, 4, 4, 4, 4, 4, 4, 2, 4, 4, 2, 4, 4, 26, 26, 26, 26, 32, 32, 32, 32, 32, 32, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119839070 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119839070/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119839070 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 132) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCCN(C)C)cc2)c1) `ZINC001119839070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119839070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119839070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001119839070 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCCN(C)C)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 21, 26, 26, 32, 32, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 26, 26, 26, 26, 32, 32, 32, 32, 32, 32, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119839070 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC001119839070 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119839070/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119839070/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001119839070 Building ZINC000927180139 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927180139' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927180139 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927180139 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927180139/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927180139 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/133 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)OC(C)(C)C)C[C@H]1CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC000927180139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927180139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927180139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000927180139 none C[C@@H]1CN(C(=O)OC(C)(C)C)C[C@H]1CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 47, 47, 50, 50, 50, 50, 28, 23, 28, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 55, 50, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927180139 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927180139/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927180139 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/134 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/134' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)OC(C)(C)C)C[C@H]1CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC000927180139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927180139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927180139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000927180139 none C[C@@H]1CN(C(=O)OC(C)(C)C)C[C@H]1CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 48, 50, 50, 50, 50, 29, 25, 29, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 18, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 55, 50, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 183 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927180139 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000927180139 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927180139/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927180139/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927180139 Building ZINC000927180139 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927180139' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927180139 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927180139 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927180139/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927180139 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 133) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1CN(C(=O)OC(C)(C)C)C[C@H]1CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC000927180139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927180139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927180139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000927180139 none C[C@@H]1CN(C(=O)OC(C)(C)C)C[C@H]1CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 47, 47, 50, 50, 50, 50, 28, 23, 28, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 55, 50, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927180139 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927180139/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927180139 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 134) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1CN(C(=O)OC(C)(C)C)C[C@H]1CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC000927180139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927180139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927180139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000927180139 none C[C@@H]1CN(C(=O)OC(C)(C)C)C[C@H]1CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 48, 50, 50, 50, 50, 29, 25, 29, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 18, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 55, 50, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 183 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927180139 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000927180139 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927180139/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927180139/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927180139 Building ZINC000428700437 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428700437' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428700437 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428700437 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428700437/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428700437 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/135 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1ccnc1CCCN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000428700437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428700437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428700437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000428700437 none CCCn1ccnc1CCCN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 8, 1, 5, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 36, 36, 36, 36, 24, 17, 13, 5, 2, 5, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 36, 36, 24, 23, 18, 18, 13, 13, 5, 5, 5, 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, 44, 45]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428700437 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428700437/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428700437 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/136 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/136' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1ccnc1CCCN(C)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000428700437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428700437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428700437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000428700437 none CCCn1ccnc1CCCN(C)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 8, 1, 5, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 24, 17, 13, 5, 2, 5, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 37, 37, 23, 24, 18, 18, 13, 13, 5, 5, 5, 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, 44, 45]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428700437 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428700437 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428700437/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428700437/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428700437 Building ZINC000428700437 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428700437' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428700437 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428700437 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428700437/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428700437 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 135) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/135: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1ccnc1CCCN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000428700437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428700437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428700437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000428700437 none CCCn1ccnc1CCCN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 8, 1, 5, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 36, 36, 36, 36, 24, 17, 13, 5, 2, 5, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 36, 36, 24, 23, 18, 18, 13, 13, 5, 5, 5, 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, 44, 45]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428700437 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428700437/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428700437 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 136) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/136: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1ccnc1CCCN(C)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000428700437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428700437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428700437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000428700437 none CCCn1ccnc1CCCN(C)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 8, 1, 5, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 24, 17, 13, 5, 2, 5, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 37, 37, 23, 24, 18, 18, 13, 13, 5, 5, 5, 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, 44, 45]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428700437 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428700437 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428700437/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428700437/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428700437 Building ZINC000152136873 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000152136873' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000152136873 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000152136873 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000152136873/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000152136873 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/137 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H](c3cccs3)C2)cc1) `ZINC000152136873.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152136873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000152136873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000152136873 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H](c3cccs3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 2, 5, 6, 10, 10, 10, 10, 10, 10, 49, 49, 49, 49, 10, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 49, 49, 49, 10, 10, 4, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000152136873 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000152136873/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000152136873 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/138 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/138' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H](c3cccs3)C2)cc1) `ZINC000152136873.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152136873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000152136873/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000152136873 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H](c3cccs3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 2, 5, 6, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 10, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 50, 50, 50, 10, 10, 5, 5] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000152136873 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000152136873 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000152136873/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000152136873/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000152136873 Building ZINC000152136873 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000152136873' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000152136873 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000152136873 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000152136873/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000152136873 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 137) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H](c3cccs3)C2)cc1) `ZINC000152136873.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152136873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000152136873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000152136873 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H](c3cccs3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 2, 5, 6, 10, 10, 10, 10, 10, 10, 49, 49, 49, 49, 10, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 49, 49, 49, 10, 10, 4, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000152136873 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000152136873/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000152136873 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 138) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H](c3cccs3)C2)cc1) `ZINC000152136873.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152136873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000152136873/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000152136873 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H](c3cccs3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 2, 5, 6, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 10, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 50, 50, 50, 10, 10, 5, 5] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000152136873 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000152136873 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000152136873/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000152136873/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000152136873 Building ZINC000428708577 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428708577' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428708577 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428708577 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428708577/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428708577 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/139 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(=O)Nc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428708577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428708577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428708577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428708577 none O=C(N1CCC(=O)Nc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 6, 4, 7, 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: [11, 2, 17, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 10, 10, 10, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428708577 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428708577/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428708577 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/140 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/140' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(=O)Nc2ccccc21)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428708577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428708577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428708577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428708577 none O=C(N1CCC(=O)Nc2ccccc21)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 6, 4, 7, 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: [11, 2, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428708577 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428708577 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428708577/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428708577/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428708577 Building ZINC000428708577 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428708577' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428708577 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428708577 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428708577/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428708577 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 139) grep: /scratch/xiaobo/83235/xao-8058115.15/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(N1CCC(=O)Nc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428708577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428708577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428708577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428708577 none O=C(N1CCC(=O)Nc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 6, 4, 7, 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: [11, 2, 17, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 10, 10, 10, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428708577 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428708577/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428708577 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 140) grep: /scratch/xiaobo/83235/xao-8058115.15/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(N1CCC(=O)Nc2ccccc21)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428708577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428708577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428708577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428708577 none O=C(N1CCC(=O)Nc2ccccc21)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 6, 4, 7, 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: [11, 2, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428708577 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428708577 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428708577/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428708577/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428708577 Building ZINC000428711009 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711009' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711009 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428711009 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711009/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711009 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/141 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccccc2)C1=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428711009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428711009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000428711009 none O=C(N[C@H]1CCN(c2ccccc2)C1=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 9, 24, 24, 24, 24, 24, 34, 34, 24, 34, 34, 24, 24, 1, 1, 1, 9, 9, 9, 9, 9, 5, 24, 24, 24, 24, 34, 34, 24, 34, 34, 9, 9] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711009 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711009/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711009 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/142 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/142' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccccc2)C1=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428711009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428711009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000428711009 none O=C(N[C@H]1CCN(c2ccccc2)C1=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 9, 22, 22, 22, 22, 22, 27, 27, 22, 27, 27, 22, 22, 1, 1, 1, 10, 10, 10, 10, 10, 5, 22, 22, 22, 22, 27, 27, 22, 27, 27, 10, 10] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711009 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428711009 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711009/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711009/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711009 Building ZINC000428711009 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711009' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711009 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428711009 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711009/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711009 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 141) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H]1CCN(c2ccccc2)C1=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428711009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428711009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000428711009 none O=C(N[C@H]1CCN(c2ccccc2)C1=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 9, 24, 24, 24, 24, 24, 34, 34, 24, 34, 34, 24, 24, 1, 1, 1, 9, 9, 9, 9, 9, 5, 24, 24, 24, 24, 34, 34, 24, 34, 34, 9, 9] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711009 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711009/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711009 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 142) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H]1CCN(c2ccccc2)C1=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428711009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428711009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000428711009 none O=C(N[C@H]1CCN(c2ccccc2)C1=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 9, 22, 22, 22, 22, 22, 27, 27, 22, 27, 27, 22, 22, 1, 1, 1, 10, 10, 10, 10, 10, 5, 22, 22, 22, 22, 27, 27, 22, 27, 27, 10, 10] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711009 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428711009 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711009/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711009/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711009 Building ZINC000428711583 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711583' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711583 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428711583 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711583/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711583 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/143 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1ncccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428711583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428711583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428711583 none COCCOc1ncccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 42, 41, 24, 6, 6, 6, 6, 6, 6, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 44, 44, 44, 42, 42, 41, 41, 6, 6, 6, 4, 8, 8] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711583 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711583/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711583 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/144 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/144' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1ncccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428711583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428711583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428711583 none COCCOc1ncccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 42, 41, 24, 6, 6, 6, 6, 6, 6, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 44, 44, 44, 42, 42, 41, 41, 6, 6, 6, 4, 8, 8] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711583 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428711583 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711583/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711583/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711583 Building ZINC000428711583 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711583' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711583 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428711583 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711583/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711583 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 143) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COCCOc1ncccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428711583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428711583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428711583 none COCCOc1ncccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 42, 41, 24, 6, 6, 6, 6, 6, 6, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 44, 44, 44, 42, 42, 41, 41, 6, 6, 6, 4, 8, 8] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711583 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711583/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711583 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 144) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COCCOc1ncccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428711583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428711583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428711583 none COCCOc1ncccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 42, 41, 24, 6, 6, 6, 6, 6, 6, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 44, 44, 44, 42, 42, 41, 41, 6, 6, 6, 4, 8, 8] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711583 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428711583 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711583/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711583/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711583 Building ZINC000622200855 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000622200855' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000622200855 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000622200855 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000622200855/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000622200855 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/145 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@@H]1CC1(F)F)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000622200855.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000622200855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000622200855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000622200855 none O=C(NCC[C@@H]1CC1(F)F)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', '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, 5, 5, 7, 5, 5, 15, 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, 17, 25, 48, 48, 48, 48, 48, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 17, 17, 31, 31, 48, 48, 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: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000622200855 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000622200855/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000622200855 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/146 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/146' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@@H]1CC1(F)F)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000622200855.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000622200855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000622200855/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000622200855 none O=C(NCC[C@@H]1CC1(F)F)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', '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, 5, 5, 7, 5, 5, 15, 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: [3, 1, 3, 3, 17, 22, 47, 47, 47, 47, 47, 1, 1, 1, 3, 3, 1, 3, 3, 3, 3, 17, 17, 30, 30, 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: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000622200855 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000622200855 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000622200855/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000622200855/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000622200855 Building ZINC000622200855 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000622200855' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000622200855 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000622200855 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000622200855/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000622200855 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 145) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NCC[C@@H]1CC1(F)F)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000622200855.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000622200855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000622200855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000622200855 none O=C(NCC[C@@H]1CC1(F)F)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', '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, 5, 5, 7, 5, 5, 15, 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, 17, 25, 48, 48, 48, 48, 48, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 17, 17, 31, 31, 48, 48, 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: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000622200855 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000622200855/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000622200855 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 146) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NCC[C@@H]1CC1(F)F)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000622200855.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000622200855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000622200855/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000622200855 none O=C(NCC[C@@H]1CC1(F)F)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', '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, 5, 5, 7, 5, 5, 15, 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: [3, 1, 3, 3, 17, 22, 47, 47, 47, 47, 47, 1, 1, 1, 3, 3, 1, 3, 3, 3, 3, 17, 17, 30, 30, 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: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000622200855 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000622200855 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000622200855/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000622200855/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000622200855 Building ZINC000428731356 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428731356' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428731356 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428731356 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428731356/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428731356 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/147 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000428731356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428731356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428731356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000428731356 none Cc1cnccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.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', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 5, 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, 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: [47, 47, 47, 43, 47, 47, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 47, 47, 47, 47, 47, 47, 20, 20, 4, 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]) total number of confs: 131 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428731356 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428731356/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428731356 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/148 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/148' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000428731356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428731356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428731356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000428731356 none Cc1cnccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.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', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 5, 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, 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: [47, 47, 47, 33, 47, 47, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 47, 47, 47, 47, 47, 47, 20, 20, 4, 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]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428731356 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428731356 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428731356/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428731356/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428731356 Building ZINC000428731356 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428731356' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428731356 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428731356 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428731356/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428731356 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 147) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/147: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000428731356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428731356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428731356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000428731356 none Cc1cnccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.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', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 5, 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, 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: [47, 47, 47, 43, 47, 47, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 47, 47, 47, 47, 47, 47, 20, 20, 4, 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]) total number of confs: 131 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428731356 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428731356/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428731356 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 148) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000428731356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428731356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428731356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000428731356 none Cc1cnccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.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', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 5, 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, 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: [47, 47, 47, 33, 47, 47, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 47, 47, 47, 47, 47, 47, 20, 20, 4, 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]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428731356 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428731356 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428731356/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428731356/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428731356 Building ZINC000174612921 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174612921' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174612921 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174612921 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174612921/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174612921 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/149 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3cc(F)ccc3n2C)cc1) `ZINC000174612921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174612921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174612921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000174612921 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3cc(F)ccc3n2C)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', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 15, 1, 1, 1, 8, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [12, 1, 1, 12, 12, 1, 1, 1, 1, 8, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 12, 12, 12, 12, 12, 12, 12, 8, 16, 16, 16, 16, 16, 16, 12, 12] 28 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174612921 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174612921/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174612921 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/150 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/150' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3cc(F)ccc3n2C)cc1) `ZINC000174612921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174612921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174612921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000174612921 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3cc(F)ccc3n2C)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', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 15, 1, 1, 1, 8, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 1, 1, 1, 1, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12, 12, 12, 8, 18, 18, 18, 18, 18, 18, 12, 12] 28 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174612921 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174612921 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174612921/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174612921/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174612921 Building ZINC000174612921 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174612921' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174612921 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174612921 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174612921/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174612921 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 149) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3cc(F)ccc3n2C)cc1) `ZINC000174612921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174612921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174612921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000174612921 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3cc(F)ccc3n2C)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', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 15, 1, 1, 1, 8, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [12, 1, 1, 12, 12, 1, 1, 1, 1, 8, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 12, 12, 12, 12, 12, 12, 12, 8, 16, 16, 16, 16, 16, 16, 12, 12] 28 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174612921 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174612921/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174612921 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 150) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3cc(F)ccc3n2C)cc1) `ZINC000174612921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174612921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174612921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000174612921 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3cc(F)ccc3n2C)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', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 15, 1, 1, 1, 8, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 1, 1, 1, 1, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12, 12, 12, 8, 18, 18, 18, 18, 18, 18, 12, 12] 28 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174612921 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174612921 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174612921/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174612921/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174612921 Building ZINC000171252025 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171252025' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171252025 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171252025 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171252025/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171252025 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/151 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1) `ZINC000171252025.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171252025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171252025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000171252025 none COC(=O)c1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 15, 15, 3, 3, 3, 3, 3, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171252025 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171252025/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171252025 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/152 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/152' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1) `ZINC000171252025.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171252025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171252025/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000171252025 none COC(=O)c1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 50, 50, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 15, 15, 3, 3, 3, 3, 3, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171252025 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000171252025 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171252025/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171252025/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171252025 Building ZINC000171252025 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171252025' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171252025 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171252025 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171252025/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171252025 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 151) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/151: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1) `ZINC000171252025.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171252025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171252025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000171252025 none COC(=O)c1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 15, 15, 3, 3, 3, 3, 3, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171252025 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171252025/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171252025 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 152) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/152: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1) `ZINC000171252025.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171252025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171252025/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000171252025 none COC(=O)c1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 50, 50, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 15, 15, 3, 3, 3, 3, 3, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171252025 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000171252025 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171252025/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171252025/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171252025 Building ZINC000337126179 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337126179' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337126179 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337126179 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337126179/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337126179 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/153 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)c(C)c(OC)c1) `ZINC000337126179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337126179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337126179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000337126179 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)c(C)c(OC)c1 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', 'O.3', 'C.3', 'C.ar', '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, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 5, 1, 12, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 6, 1, 1, 1, 6, 6, 2, 6, 6, 6, 7, 20, 20, 20, 20, 35, 20, 28, 28, 28, 20, 6, 6, 6, 6, 6, 7, 7, 7, 20, 20, 20, 35, 35, 35, 20] 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: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337126179 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337126179/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337126179 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/154 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/154' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)c(C)c(OC)c1) `ZINC000337126179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337126179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337126179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000337126179 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)c(C)c(OC)c1 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', 'O.3', 'C.3', 'C.ar', '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, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 5, 1, 12, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 6, 1, 1, 1, 6, 6, 2, 6, 6, 6, 7, 20, 20, 20, 20, 35, 20, 28, 28, 28, 20, 6, 6, 6, 6, 6, 7, 7, 7, 20, 20, 20, 35, 35, 35, 20] 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: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337126179 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337126179 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337126179/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337126179/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337126179 Building ZINC000337126179 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337126179' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337126179 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337126179 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337126179/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337126179 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 153) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)c(C)c(OC)c1) `ZINC000337126179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337126179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337126179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000337126179 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)c(C)c(OC)c1 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', 'O.3', 'C.3', 'C.ar', '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, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 5, 1, 12, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 6, 1, 1, 1, 6, 6, 2, 6, 6, 6, 7, 20, 20, 20, 20, 35, 20, 28, 28, 28, 20, 6, 6, 6, 6, 6, 7, 7, 7, 20, 20, 20, 35, 35, 35, 20] 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: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337126179 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337126179/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337126179 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 154) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1cc(NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)c(C)c(OC)c1) `ZINC000337126179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337126179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337126179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000337126179 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)c(C)c(OC)c1 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', 'O.3', 'C.3', 'C.ar', '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, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 5, 1, 12, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 6, 1, 1, 1, 6, 6, 2, 6, 6, 6, 7, 20, 20, 20, 20, 35, 20, 28, 28, 28, 20, 6, 6, 6, 6, 6, 7, 7, 7, 20, 20, 20, 35, 35, 35, 20] 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: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337126179 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337126179 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337126179/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337126179/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337126179 Building ZINC000171270061 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171270061' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171270061 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171270061 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171270061/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171270061 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/155 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1ccc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171270061.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171270061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171270061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000171270061 none NC(=O)c1ccc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', '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', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 47, 27, 27, 5, 27, 27, 27, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 5, 5, 5, 47, 47, 27, 27, 27, 5, 5, 5, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 179 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171270061 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171270061/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171270061 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/156 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/156' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1ccc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171270061.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171270061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171270061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000171270061 none NC(=O)c1ccc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', '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', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 28, 28, 5, 28, 28, 28, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 47, 47, 28, 28, 28, 5, 5, 5, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 175 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171270061 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000171270061 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171270061/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171270061/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171270061 Building ZINC000171270061 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171270061' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171270061 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171270061 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171270061/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171270061 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 155) grep: /scratch/xiaobo/83235/xao-8058115.15/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: NC(=O)c1ccc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171270061.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171270061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171270061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000171270061 none NC(=O)c1ccc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', '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', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 47, 27, 27, 5, 27, 27, 27, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 5, 5, 5, 47, 47, 27, 27, 27, 5, 5, 5, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 179 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171270061 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171270061/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171270061 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 156) grep: /scratch/xiaobo/83235/xao-8058115.15/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: NC(=O)c1ccc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171270061.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171270061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171270061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000171270061 none NC(=O)c1ccc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', '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', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 28, 28, 5, 28, 28, 28, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 47, 47, 28, 28, 28, 5, 5, 5, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 175 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171270061 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000171270061 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171270061/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171270061/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171270061 Building ZINC000171272513 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000171272513 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/157 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171272513.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171272513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171272513 none O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)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', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 20, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 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, 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/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/158 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/158' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171272513.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171272513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171272513 none O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)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', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 20, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 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, 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/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/159 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/159' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171272513.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000171272513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171272513 none O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)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', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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 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, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 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: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/160 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/160' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171272513.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000171272513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171272513 none O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)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', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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 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, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 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: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000171272513 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 Building ZINC000171272513 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000171272513 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 157) grep: /scratch/xiaobo/83235/xao-8058115.15/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[C@H]1CC[N@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171272513.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171272513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171272513 none O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)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', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 20, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 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, 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/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 158) grep: /scratch/xiaobo/83235/xao-8058115.15/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[C@H]1CC[N@@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171272513.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171272513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171272513 none O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)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', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 20, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 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, 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/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 159) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/159: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171272513.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000171272513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171272513 none O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)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', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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 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, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 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: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 160) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/160: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171272513.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000171272513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171272513 none O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)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', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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 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, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 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: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000171272513 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 Building ZINC000171272513 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000171272513 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 157) grep: /scratch/xiaobo/83235/xao-8058115.15/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[C@H]1CC[N@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171272513.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171272513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171272513 none O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)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', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 20, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 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, 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/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 158) grep: /scratch/xiaobo/83235/xao-8058115.15/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[C@H]1CC[N@@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171272513.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171272513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171272513 none O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)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', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 20, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 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, 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/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 159) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/159: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171272513.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000171272513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171272513 none O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)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', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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 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, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 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: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 160) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/160: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171272513.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000171272513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171272513 none O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)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', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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 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, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 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: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000171272513 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 Building ZINC000171272513 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000171272513 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 157) grep: /scratch/xiaobo/83235/xao-8058115.15/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[C@H]1CC[N@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171272513.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171272513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171272513 none O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)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', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 20, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 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, 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/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 158) grep: /scratch/xiaobo/83235/xao-8058115.15/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[C@H]1CC[N@@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171272513.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171272513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171272513 none O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)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', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 20, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 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, 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/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 159) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/159: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171272513.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000171272513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171272513 none O=C(N[C@H]1CC[N@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)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', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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 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, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 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: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 160) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/160: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171272513.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000171272513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171272513 none O=C(N[C@H]1CC[N@@](c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)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', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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 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, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 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: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000171272513 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171272513 Building ZINC000337127754 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127754' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127754 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337127754 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127754/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127754 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/161 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](c3ccccc3F)C2)cn1) `ZINC000337127754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337127754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337127754 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](c3ccccc3F)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 4, 12, 12, 4, 4, 1, 1, 1, 1, 2, 3, 9, 9, 9, 9, 9, 21, 21, 9, 21, 21, 21, 9, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 9, 9, 9, 9, 21, 21, 20, 21, 9, 9, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127754 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127754/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127754 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/162 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/162' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](c3ccccc3F)C2)cn1) `ZINC000337127754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337127754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337127754 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](c3ccccc3F)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 2, 4, 11, 11, 11, 11, 11, 33, 33, 11, 33, 33, 33, 11, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 11, 11, 11, 11, 33, 33, 15, 33, 11, 11, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 107 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127754 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337127754 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127754/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127754/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127754 Building ZINC000337127754 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127754' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127754 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337127754 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127754/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127754 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 161) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](c3ccccc3F)C2)cn1) `ZINC000337127754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337127754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337127754 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](c3ccccc3F)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 4, 12, 12, 4, 4, 1, 1, 1, 1, 2, 3, 9, 9, 9, 9, 9, 21, 21, 9, 21, 21, 21, 9, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 9, 9, 9, 9, 21, 21, 20, 21, 9, 9, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127754 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127754/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127754 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 162) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/162: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](c3ccccc3F)C2)cn1) `ZINC000337127754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337127754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337127754 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](c3ccccc3F)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 2, 4, 11, 11, 11, 11, 11, 33, 33, 11, 33, 33, 33, 11, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 11, 11, 11, 11, 33, 33, 15, 33, 11, 11, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 107 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127754 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337127754 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127754/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127754/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127754 Building ZINC000337127755 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127755' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127755 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337127755 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127755/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127755 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/163 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](c3ccccc3F)C2)cn1) `ZINC000337127755.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337127755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337127755 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](c3ccccc3F)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 2, 3, 10, 10, 10, 10, 10, 28, 28, 10, 28, 28, 28, 10, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 10, 10, 10, 10, 28, 28, 28, 28, 10, 10, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 116 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127755 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127755/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127755 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/164 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/164' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](c3ccccc3F)C2)cn1) `ZINC000337127755.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337127755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127755/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337127755 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](c3ccccc3F)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 11, 11, 5, 5, 1, 1, 1, 1, 2, 3, 10, 10, 10, 10, 10, 26, 26, 16, 26, 26, 26, 10, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 10, 10, 10, 10, 26, 26, 26, 26, 10, 10, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 103 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127755 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337127755 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127755/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127755/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127755 Building ZINC000337127755 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127755' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127755 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337127755 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127755/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127755 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 163) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](c3ccccc3F)C2)cn1) `ZINC000337127755.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337127755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337127755 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](c3ccccc3F)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 2, 3, 10, 10, 10, 10, 10, 28, 28, 10, 28, 28, 28, 10, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 10, 10, 10, 10, 28, 28, 28, 28, 10, 10, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 116 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127755 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127755/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127755 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 164) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](c3ccccc3F)C2)cn1) `ZINC000337127755.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337127755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127755/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337127755 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](c3ccccc3F)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 11, 11, 5, 5, 1, 1, 1, 1, 2, 3, 10, 10, 10, 10, 10, 26, 26, 16, 26, 26, 26, 10, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 10, 10, 10, 10, 26, 26, 26, 26, 10, 10, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 103 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127755 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337127755 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127755/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127755/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337127755 Building ZINC000171286518 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286518' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286518 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171286518 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286518/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286518 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/165 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccccc1) `ZINC000171286518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171286518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000171286518 none COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 32, 6, 12, 6, 1, 6, 1, 1, 1, 5, 5, 2, 5, 5, 5, 12, 27, 27, 12, 27, 27, 32, 32, 32, 6, 5, 5, 5, 5, 27, 27, 12, 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]) total number of confs: 185 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286518 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286518/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286518 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/166 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/166' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccccc1) `ZINC000171286518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171286518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000171286518 none COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 6, 11, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 11, 25, 25, 11, 25, 25, 30, 30, 30, 6, 5, 5, 5, 5, 25, 25, 11, 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]) total number of confs: 166 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286518 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000171286518 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286518/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286518/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286518 Building ZINC000171286518 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286518' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286518 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171286518 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286518/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286518 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 165) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccccc1) `ZINC000171286518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171286518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000171286518 none COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 32, 6, 12, 6, 1, 6, 1, 1, 1, 5, 5, 2, 5, 5, 5, 12, 27, 27, 12, 27, 27, 32, 32, 32, 6, 5, 5, 5, 5, 27, 27, 12, 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]) total number of confs: 185 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286518 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286518/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286518 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 166) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccccc1) `ZINC000171286518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171286518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000171286518 none COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 6, 11, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 11, 25, 25, 11, 25, 25, 30, 30, 30, 6, 5, 5, 5, 5, 25, 25, 11, 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]) total number of confs: 166 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286518 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000171286518 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286518/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286518/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286518 Building ZINC000171286523 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286523' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286523 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171286523 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286523/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286523 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/167 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccccc1) `ZINC000171286523.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171286523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000171286523 none COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 6, 11, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 11, 25, 25, 11, 25, 25, 30, 30, 30, 6, 5, 5, 5, 5, 25, 25, 11, 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]) total number of confs: 166 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286523 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286523/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286523 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/168 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/168' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccccc1) `ZINC000171286523.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171286523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286523/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000171286523 none COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 32, 6, 12, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 12, 27, 27, 12, 27, 27, 32, 32, 32, 6, 5, 5, 5, 5, 27, 27, 12, 27, 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]) total number of confs: 182 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286523 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000171286523 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286523/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286523/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286523 Building ZINC000171286523 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286523' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286523 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171286523 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286523/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286523 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 167) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccccc1) `ZINC000171286523.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171286523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000171286523 none COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 6, 11, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 11, 25, 25, 11, 25, 25, 30, 30, 30, 6, 5, 5, 5, 5, 25, 25, 11, 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]) total number of confs: 166 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286523 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286523/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286523 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 168) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccccc1) `ZINC000171286523.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171286523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286523/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000171286523 none COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 32, 6, 12, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 12, 27, 27, 12, 27, 27, 32, 32, 32, 6, 5, 5, 5, 5, 27, 27, 12, 27, 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]) total number of confs: 182 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286523 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000171286523 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286523/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286523/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171286523 Building ZINC000337132093 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132093' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132093 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337132093 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132093/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132093 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/169 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1ccnn1C) `ZINC000337132093.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337132093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000337132093 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 19, 19, 25, 25, 25, 25, 25, 25, 25, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 89 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132093 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132093/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132093 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/170 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/170' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1ccnn1C) `ZINC000337132093.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337132093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132093/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000337132093 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 18, 18, 26, 26, 26, 26, 26, 26, 26, 40, 40, 40, 40, 40, 5, 5, 5, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 40, 40, 40, 40, 40] 41 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 80 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132093 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337132093 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132093/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132093/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132093 Building ZINC000337132093 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132093' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132093 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337132093 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132093/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132093 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 169) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/169: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1ccnn1C) `ZINC000337132093.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337132093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000337132093 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 19, 19, 25, 25, 25, 25, 25, 25, 25, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 89 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132093 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132093/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132093 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 170) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/170: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1ccnn1C) `ZINC000337132093.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337132093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132093/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000337132093 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 18, 18, 26, 26, 26, 26, 26, 26, 26, 40, 40, 40, 40, 40, 5, 5, 5, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 40, 40, 40, 40, 40] 41 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 80 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132093 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337132093 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132093/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132093/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132093 Building ZINC000337132097 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132097' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132097 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337132097 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132097/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132097 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/171 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1ccnn1C) `ZINC000337132097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337132097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000337132097 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 19, 19, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 50, 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, 42, 43]) total number of confs: 93 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132097 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132097/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132097 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/172 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/172' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1ccnn1C) `ZINC000337132097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337132097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000337132097 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 18, 18, 24, 24, 24, 24, 24, 24, 24, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 24, 24, 24, 24, 24, 24, 24, 24, 46, 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]) total number of confs: 86 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132097 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337132097 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132097/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132097/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132097 Building ZINC000337132097 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132097' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132097 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337132097 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132097/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132097 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 171) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1ccnn1C) `ZINC000337132097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337132097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000337132097 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 19, 19, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 50, 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, 42, 43]) total number of confs: 93 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132097 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132097/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132097 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 172) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1ccnn1C) `ZINC000337132097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337132097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000337132097 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 18, 18, 24, 24, 24, 24, 24, 24, 24, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 24, 24, 24, 24, 24, 24, 24, 24, 46, 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]) total number of confs: 86 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132097 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337132097 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132097/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132097/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337132097 Building ZINC000171294899 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171294899' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171294899 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171294899 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171294899/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171294899 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/173 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(c2ccncc2)n[nH]1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000171294899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171294899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171294899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000171294899 none O=C(Nc1cc(c2ccncc2)n[nH]1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 6, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 13, 13, 13, 13, 31, 31, 13, 31, 31, 13, 13, 13, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 31, 31, 31, 31, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171294899 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171294899/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171294899 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/174 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/174' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(c2ccncc2)n[nH]1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000171294899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171294899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171294899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000171294899 none O=C(Nc1cc(c2ccncc2)n[nH]1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 6, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 13, 13, 13, 13, 32, 32, 32, 32, 32, 13, 13, 13, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 32, 32, 32, 32, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171294899 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000171294899 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171294899/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171294899/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171294899 Building ZINC000171294899 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171294899' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171294899 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171294899 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171294899/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171294899 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 173) grep: /scratch/xiaobo/83235/xao-8058115.15/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(Nc1cc(c2ccncc2)n[nH]1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000171294899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171294899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171294899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000171294899 none O=C(Nc1cc(c2ccncc2)n[nH]1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 6, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 13, 13, 13, 13, 31, 31, 13, 31, 31, 13, 13, 13, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 31, 31, 31, 31, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171294899 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171294899/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171294899 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 174) grep: /scratch/xiaobo/83235/xao-8058115.15/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(Nc1cc(c2ccncc2)n[nH]1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000171294899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171294899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171294899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000171294899 none O=C(Nc1cc(c2ccncc2)n[nH]1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 6, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 13, 13, 13, 13, 32, 32, 32, 32, 32, 13, 13, 13, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 32, 32, 32, 32, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171294899 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000171294899 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171294899/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171294899/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171294899 Building ZINC000428793669 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793669' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793669 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428793669 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793669/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793669 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/175 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21) `ZINC000428793669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428793669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000428793669 none NC(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 17, 32, 17, 17, 17, 17, 12, 3, 14, 1, 1, 1, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 32, 32, 17, 17, 17, 17, 8, 8, 17, 17, 17, 17] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 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, 31, 32, 33, 34, 35]) total number of confs: 98 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793669 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793669/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793669 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/176 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/176' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21) `ZINC000428793669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428793669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000428793669 none NC(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 33, 18, 18, 18, 18, 12, 3, 15, 1, 1, 1, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 33, 33, 18, 18, 18, 18, 7, 7, 18, 18, 18, 18] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 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, 31, 32, 33, 34, 35]) total number of confs: 96 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793669 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428793669 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793669/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793669/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793669 Building ZINC000428793669 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793669' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793669 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428793669 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793669/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793669 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 175) grep: /scratch/xiaobo/83235/xao-8058115.15/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: NC(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21) `ZINC000428793669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428793669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000428793669 none NC(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 17, 32, 17, 17, 17, 17, 12, 3, 14, 1, 1, 1, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 32, 32, 17, 17, 17, 17, 8, 8, 17, 17, 17, 17] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 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, 31, 32, 33, 34, 35]) total number of confs: 98 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793669 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793669/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793669 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 176) grep: /scratch/xiaobo/83235/xao-8058115.15/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: NC(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21) `ZINC000428793669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428793669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000428793669 none NC(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 33, 18, 18, 18, 18, 12, 3, 15, 1, 1, 1, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 33, 33, 18, 18, 18, 18, 7, 7, 18, 18, 18, 18] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 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, 31, 32, 33, 34, 35]) total number of confs: 96 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793669 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428793669 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793669/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793669/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793669 Building ZINC000428793671 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793671' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793671 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428793671 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793671/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793671 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/177 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21) `ZINC000428793671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428793671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000428793671 none NC(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 34, 20, 20, 20, 20, 14, 3, 15, 1, 1, 1, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 20, 34, 34, 20, 20, 20, 20, 8, 8, 20, 20, 20, 20] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 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, 31, 32, 33, 34, 35]) total number of confs: 95 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793671 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793671/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793671 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/178 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/178' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21) `ZINC000428793671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428793671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000428793671 none NC(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 32, 20, 20, 20, 20, 14, 3, 16, 1, 1, 1, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 20, 32, 32, 20, 20, 20, 20, 8, 8, 20, 20, 20, 20] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 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, 31, 32, 33, 34, 35]) total number of confs: 95 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793671 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428793671 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793671/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793671/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793671 Building ZINC000428793671 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793671' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793671 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428793671 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793671/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793671 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 177) grep: /scratch/xiaobo/83235/xao-8058115.15/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: NC(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21) `ZINC000428793671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428793671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000428793671 none NC(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 34, 20, 20, 20, 20, 14, 3, 15, 1, 1, 1, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 20, 34, 34, 20, 20, 20, 20, 8, 8, 20, 20, 20, 20] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 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, 31, 32, 33, 34, 35]) total number of confs: 95 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793671 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793671/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793671 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 178) grep: /scratch/xiaobo/83235/xao-8058115.15/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: NC(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21) `ZINC000428793671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428793671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000428793671 none NC(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 32, 20, 20, 20, 20, 14, 3, 16, 1, 1, 1, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 20, 32, 32, 20, 20, 20, 20, 8, 8, 20, 20, 20, 20] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 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, 31, 32, 33, 34, 35]) total number of confs: 95 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793671 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428793671 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793671/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793671/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428793671 Building ZINC000195098579 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000195098579' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000195098579 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195098579 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000195098579/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000195098579 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/179 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/179' -> `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)c1)c1ccc(Cl)c(Cl)c1) `ZINC000195098579.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195098579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000195098579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000195098579 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 8, 34, 34, 34, 34, 34, 34, 34, 8, 8, 8, 4, 7, 7, 7, 7, 7, 34, 34, 34] 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]) total number of confs: 74 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000195098579 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000195098579/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000195098579 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/180 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/180' -> `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)c1)c1ccc(Cl)c(Cl)c1) `ZINC000195098579.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195098579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000195098579/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000195098579 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 8, 34, 34, 19, 34, 34, 34, 34, 8, 8, 8, 4, 7, 7, 7, 7, 7, 34, 34, 34] 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]) total number of confs: 122 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000195098579 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000195098579 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000195098579/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000195098579/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000195098579 Building ZINC000195098579 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000195098579' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000195098579 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195098579 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000195098579/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000195098579 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 179) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1ccc(Cl)c(Cl)c1) `ZINC000195098579.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195098579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000195098579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000195098579 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 8, 34, 34, 34, 34, 34, 34, 34, 8, 8, 8, 4, 7, 7, 7, 7, 7, 34, 34, 34] 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]) total number of confs: 74 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000195098579 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000195098579/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000195098579 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 180) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1ccc(Cl)c(Cl)c1) `ZINC000195098579.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195098579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000195098579/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000195098579 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 8, 34, 34, 19, 34, 34, 34, 34, 8, 8, 8, 4, 7, 7, 7, 7, 7, 34, 34, 34] 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]) total number of confs: 122 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000195098579 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000195098579 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000195098579/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000195098579/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000195098579 Building ZINC000927280293 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280293' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280293 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927280293 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280293/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280293 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/181 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@]2(CC(F)(F)C2(F)F)C1) `ZINC000927280293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927280293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000927280293 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@]2(CC(F)(F)C2(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 15, 15, 5, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 4, 7, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 21, 5, 5, 5, 5, 5, 5, 5, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280293 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280293/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280293 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/182 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/182' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@]2(CC(F)(F)C2(F)F)C1) `ZINC000927280293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927280293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000927280293 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@]2(CC(F)(F)C2(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 15, 15, 5, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 4, 7, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 24, 5, 5, 5, 5, 5, 5, 5, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280293 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000927280293 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280293/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280293/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280293 Building ZINC000927280293 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280293' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280293 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927280293 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280293/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280293 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 181) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@]2(CC(F)(F)C2(F)F)C1) `ZINC000927280293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927280293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000927280293 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@]2(CC(F)(F)C2(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 15, 15, 5, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 4, 7, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 21, 5, 5, 5, 5, 5, 5, 5, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280293 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280293/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280293 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 182) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@]2(CC(F)(F)C2(F)F)C1) `ZINC000927280293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927280293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000927280293 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@]2(CC(F)(F)C2(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 15, 15, 5, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 4, 7, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 24, 5, 5, 5, 5, 5, 5, 5, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280293 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000927280293 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280293/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280293/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280293 Building ZINC000927280294 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280294' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280294 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927280294 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280294/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280294 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/183 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@]2(CC(F)(F)C2(F)F)C1) `ZINC000927280294.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927280294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000927280294 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@]2(CC(F)(F)C2(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 15, 15, 5, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 4, 11, 31, 37, 37, 37, 37, 37, 37, 37, 37, 37, 27, 5, 5, 5, 5, 5, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 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: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280294 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280294/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280294 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/184 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/184' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@@]2(CC(F)(F)C2(F)F)C1) `ZINC000927280294.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927280294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280294/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000927280294 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@@]2(CC(F)(F)C2(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 15, 15, 5, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 3, 9, 32, 37, 37, 37, 37, 37, 37, 37, 37, 37, 28, 5, 5, 5, 5, 5, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 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: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280294 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000927280294 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280294/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280294/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280294 Building ZINC000927280294 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280294' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280294 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927280294 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280294/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280294 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 183) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@]2(CC(F)(F)C2(F)F)C1) `ZINC000927280294.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927280294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000927280294 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@]2(CC(F)(F)C2(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 15, 15, 5, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 4, 11, 31, 37, 37, 37, 37, 37, 37, 37, 37, 37, 27, 5, 5, 5, 5, 5, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 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: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280294 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280294/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280294 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 184) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@@]2(CC(F)(F)C2(F)F)C1) `ZINC000927280294.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927280294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280294/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000927280294 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@@]2(CC(F)(F)C2(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 15, 15, 5, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 3, 9, 32, 37, 37, 37, 37, 37, 37, 37, 37, 37, 28, 5, 5, 5, 5, 5, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 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: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280294 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000927280294 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280294/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280294/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927280294 Building ZINC000428800852 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428800852' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428800852 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428800852 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428800852/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428800852 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/185 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1cnc(C2CC2)nc1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428800852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428800852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428800852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428800852 none O=C(NCCc1cnc(C2CC2)nc1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 14, 14, 14, 14, 14, 43, 43, 14, 14, 1, 1, 1, 8, 8, 8, 8, 8, 2, 9, 9, 14, 14, 14, 43, 43, 43, 43, 43, 14, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428800852 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428800852/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428800852 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/186 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/186' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1cnc(C2CC2)nc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428800852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428800852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428800852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428800852 none O=C(NCCc1cnc(C2CC2)nc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 14, 14, 14, 14, 14, 41, 41, 14, 14, 1, 1, 1, 8, 8, 8, 8, 8, 2, 10, 10, 14, 14, 14, 41, 41, 41, 41, 41, 14, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428800852 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428800852 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428800852/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428800852/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428800852 Building ZINC000428800852 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428800852' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428800852 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428800852 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428800852/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428800852 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 185) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NCCc1cnc(C2CC2)nc1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428800852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428800852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428800852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428800852 none O=C(NCCc1cnc(C2CC2)nc1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 14, 14, 14, 14, 14, 43, 43, 14, 14, 1, 1, 1, 8, 8, 8, 8, 8, 2, 9, 9, 14, 14, 14, 43, 43, 43, 43, 43, 14, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428800852 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428800852/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428800852 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 186) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NCCc1cnc(C2CC2)nc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428800852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428800852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428800852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000428800852 none O=C(NCCc1cnc(C2CC2)nc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 14, 14, 14, 14, 14, 41, 41, 14, 14, 1, 1, 1, 8, 8, 8, 8, 8, 2, 10, 10, 14, 14, 14, 41, 41, 41, 41, 41, 14, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428800852 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428800852 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428800852/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428800852/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428800852 Building ZINC000171389801 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389801' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389801 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171389801 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389801/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389801 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/187 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171389801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171389801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171389801 none CN(C)C[C@@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 41, 19, 4, 19, 19, 32, 35, 35, 34, 35, 35, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 41, 41, 41, 41, 41, 41, 37, 37, 32, 32, 35, 35, 35, 35, 35, 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, 43, 44]) total number of confs: 256 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389801 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389801/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389801 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/188 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/188' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171389801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171389801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171389801 none CN(C)C[C@@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 38, 16, 4, 16, 16, 31, 33, 33, 33, 33, 33, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 38, 38, 38, 38, 38, 38, 35, 35, 31, 31, 33, 33, 33, 33, 33, 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, 44]) total number of confs: 236 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389801 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000171389801 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389801/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389801/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389801 Building ZINC000171389801 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389801' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389801 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171389801 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389801/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389801 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 187) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/187: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171389801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171389801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171389801 none CN(C)C[C@@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 41, 19, 4, 19, 19, 32, 35, 35, 34, 35, 35, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 41, 41, 41, 41, 41, 41, 37, 37, 32, 32, 35, 35, 35, 35, 35, 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, 43, 44]) total number of confs: 256 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389801 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389801/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389801 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 188) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/188: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171389801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171389801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171389801 none CN(C)C[C@@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 38, 16, 4, 16, 16, 31, 33, 33, 33, 33, 33, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 38, 38, 38, 38, 38, 38, 35, 35, 31, 31, 33, 33, 33, 33, 33, 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, 44]) total number of confs: 236 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389801 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000171389801 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389801/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389801/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389801 Building ZINC000171389806 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389806' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389806 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171389806 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389806/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389806 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/189 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171389806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171389806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171389806 none CN(C)C[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 35, 36, 16, 4, 16, 16, 30, 32, 32, 30, 32, 32, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 36, 36, 36, 36, 36, 36, 35, 35, 30, 30, 32, 32, 32, 32, 32, 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, 44]) total number of confs: 238 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389806 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389806/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389806 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/190 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/190' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171389806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171389806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171389806 none CN(C)C[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 35, 36, 17, 4, 17, 17, 30, 34, 34, 32, 34, 34, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 36, 36, 36, 36, 36, 36, 35, 35, 30, 30, 34, 34, 34, 34, 34, 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, 44]) total number of confs: 239 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389806 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000171389806 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389806/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389806/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389806 Building ZINC000171389806 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389806' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389806 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171389806 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389806/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389806 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 189) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN(C)C[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171389806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171389806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171389806 none CN(C)C[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 35, 36, 16, 4, 16, 16, 30, 32, 32, 30, 32, 32, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 36, 36, 36, 36, 36, 36, 35, 35, 30, 30, 32, 32, 32, 32, 32, 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, 44]) total number of confs: 238 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389806 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389806/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389806 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 190) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN(C)C[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000171389806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171389806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171389806 none CN(C)C[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 35, 36, 17, 4, 17, 17, 30, 34, 34, 32, 34, 34, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 36, 36, 36, 36, 36, 36, 35, 35, 30, 30, 34, 34, 34, 34, 34, 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, 44]) total number of confs: 239 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389806 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000171389806 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389806/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389806/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171389806 Building ZINC000171403561 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171403561' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171403561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171403561 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171403561/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171403561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/191 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1noc(CCCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n1) `ZINC000171403561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171403561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171403561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000171403561 none CC(C)c1noc(CCCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 1, 8, 12, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 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, 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: [50, 48, 50, 48, 48, 48, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 50, 50, 50, 9, 9, 8, 8, 6, 6, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171403561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171403561/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171403561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/192 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/192' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1noc(CCCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n1) `ZINC000171403561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171403561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171403561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000171403561 none CC(C)c1noc(CCCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 1, 8, 12, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 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, 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: [50, 49, 50, 49, 49, 49, 11, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 50, 50, 10, 10, 9, 9, 7, 7, 2, 2, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171403561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000171403561 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171403561/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171403561/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171403561 Building ZINC000171403561 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171403561' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171403561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171403561 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171403561/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171403561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 191) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/191: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1noc(CCCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n1) `ZINC000171403561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171403561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171403561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000171403561 none CC(C)c1noc(CCCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 1, 8, 12, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 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, 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: [50, 48, 50, 48, 48, 48, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 50, 50, 50, 9, 9, 8, 8, 6, 6, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171403561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171403561/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171403561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 192) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1noc(CCCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n1) `ZINC000171403561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171403561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171403561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000171403561 none CC(C)c1noc(CCCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 1, 8, 12, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 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, 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: [50, 49, 50, 49, 49, 49, 11, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 50, 50, 10, 10, 9, 9, 7, 7, 2, 2, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171403561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000171403561 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171403561/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171403561/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000171403561 Building ZINC000337155580 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337155580' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337155580 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337155580 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337155580/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337155580 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/193 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCC2=O)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000337155580.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337155580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337155580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000337155580 none O=C(Nc1ccc(N2CCC2=O)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [7, 1, 7, 7, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 1, 1, 1, 6, 6, 1, 1, 6, 6, 7, 20, 20, 50, 50, 50, 50, 20, 20, 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, 35]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337155580 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337155580/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337155580 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/194 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/194' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCC2=O)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000337155580.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337155580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337155580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000337155580 none O=C(Nc1ccc(N2CCC2=O)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [7, 1, 7, 7, 20, 20, 14, 20, 50, 49, 50, 50, 20, 20, 1, 1, 1, 6, 6, 1, 1, 6, 6, 7, 20, 20, 50, 50, 50, 50, 20, 20, 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, 35]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337155580 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337155580 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337155580/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337155580/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337155580 Building ZINC000337155580 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337155580' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337155580 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337155580 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337155580/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337155580 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 193) grep: /scratch/xiaobo/83235/xao-8058115.15/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(Nc1ccc(N2CCC2=O)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000337155580.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337155580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337155580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000337155580 none O=C(Nc1ccc(N2CCC2=O)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [7, 1, 7, 7, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 1, 1, 1, 6, 6, 1, 1, 6, 6, 7, 20, 20, 50, 50, 50, 50, 20, 20, 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, 35]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337155580 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337155580/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337155580 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 194) grep: /scratch/xiaobo/83235/xao-8058115.15/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(Nc1ccc(N2CCC2=O)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000337155580.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337155580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337155580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000337155580 none O=C(Nc1ccc(N2CCC2=O)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [7, 1, 7, 7, 20, 20, 14, 20, 50, 49, 50, 50, 20, 20, 1, 1, 1, 6, 6, 1, 1, 6, 6, 7, 20, 20, 50, 50, 50, 50, 20, 20, 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, 35]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337155580 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337155580 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337155580/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337155580/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337155580 Building ZINC000575407600 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000575407600' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000575407600 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000575407600 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000575407600/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000575407600 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/195 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/195' -> `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)N1CCc2sc(Cl)cc2C1) `ZINC000575407600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000575407600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000575407600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000575407600 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2sc(Cl)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 14, 1, 16, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 6, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 5, 5, 5, 5, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21] 31 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 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: 38 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000575407600 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000575407600/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000575407600 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/196 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/196' -> `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)N1CCc2sc(Cl)cc2C1) `ZINC000575407600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000575407600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000575407600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000575407600 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2sc(Cl)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 14, 1, 16, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22] 31 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 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: 39 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000575407600 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000575407600 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000575407600/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000575407600/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000575407600 Building ZINC000575407600 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000575407600' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000575407600 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000575407600 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000575407600/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000575407600 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 195) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2sc(Cl)cc2C1) `ZINC000575407600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000575407600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000575407600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000575407600 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2sc(Cl)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 14, 1, 16, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 6, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 5, 5, 5, 5, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21] 31 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 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: 38 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000575407600 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000575407600/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000575407600 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 196) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2sc(Cl)cc2C1) `ZINC000575407600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000575407600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000575407600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000575407600 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2sc(Cl)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 14, 1, 16, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22] 31 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 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: 39 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000575407600 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000575407600 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000575407600/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000575407600/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000575407600 Building ZINC000752277511 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277511' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277511 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752277511 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277511/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277511 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/197 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C[C@H](O)c1cccs1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000752277511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752277511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000752277511 none C[C@@H](C[C@H](O)c1cccs1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 14, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 6, 6, 10, 14, 14, 14, 30, 30, 30, 30, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 12, 12, 12, 5, 6, 6, 6, 11, 11, 42, 30, 30, 30, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277511 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277511/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277511 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/198 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/198' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C[C@H](O)c1cccs1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000752277511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752277511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000752277511 none C[C@@H](C[C@H](O)c1cccs1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 14, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 7, 7, 11, 17, 17, 17, 31, 31, 31, 31, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 7, 7, 7, 12, 12, 51, 31, 31, 31, 3, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 204 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277511 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000752277511 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277511/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277511/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277511 Building ZINC000752277511 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277511' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277511 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752277511 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277511/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277511 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 197) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H](C[C@H](O)c1cccs1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000752277511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752277511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000752277511 none C[C@@H](C[C@H](O)c1cccs1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 14, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 6, 6, 10, 14, 14, 14, 30, 30, 30, 30, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 12, 12, 12, 5, 6, 6, 6, 11, 11, 42, 30, 30, 30, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277511 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277511/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277511 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 198) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H](C[C@H](O)c1cccs1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000752277511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752277511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000752277511 none C[C@@H](C[C@H](O)c1cccs1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 14, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 7, 7, 11, 17, 17, 17, 31, 31, 31, 31, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 7, 7, 7, 12, 12, 51, 31, 31, 31, 3, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 204 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277511 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000752277511 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277511/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277511/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277511 Building ZINC000752277512 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277512' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277512 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752277512 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277512/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277512 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/199 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@@H](O)c1cccs1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000752277512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752277512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000752277512 none C[C@H](C[C@@H](O)c1cccs1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 14, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 6, 6, 10, 17, 17, 17, 33, 33, 33, 33, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 6, 6, 6, 11, 11, 51, 33, 33, 33, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 204 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277512 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277512/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277512 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/200 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/200' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@@H](O)c1cccs1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000752277512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752277512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000752277512 none C[C@H](C[C@@H](O)c1cccs1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 14, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 6, 6, 10, 14, 14, 14, 31, 31, 31, 31, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 13, 13, 13, 5, 6, 6, 6, 11, 11, 42, 31, 31, 31, 3, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277512 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000752277512 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277512/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277512/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277512 Building ZINC000752277512 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277512' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277512 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752277512 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277512/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277512 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 199) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H](C[C@@H](O)c1cccs1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000752277512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752277512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000752277512 none C[C@H](C[C@@H](O)c1cccs1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 14, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 6, 6, 10, 17, 17, 17, 33, 33, 33, 33, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 6, 6, 6, 11, 11, 51, 33, 33, 33, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 204 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277512 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277512/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277512 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 200) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H](C[C@@H](O)c1cccs1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000752277512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752277512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000752277512 none C[C@H](C[C@@H](O)c1cccs1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 14, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 6, 6, 10, 14, 14, 14, 31, 31, 31, 31, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 13, 13, 13, 5, 6, 6, 6, 11, 11, 42, 31, 31, 31, 3, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277512 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000752277512 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277512/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277512/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277512 Building ZINC000752277513 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277513' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752277513 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277513/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/201 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C[C@@H](O)c1cccs1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000752277513.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752277513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000752277513 none C[C@@H](C[C@@H](O)c1cccs1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 14, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 6, 6, 10, 17, 17, 17, 37, 37, 37, 37, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 6, 6, 6, 10, 10, 51, 37, 37, 37, 2, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 201 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277513/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/202 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/202' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C[C@@H](O)c1cccs1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000752277513.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752277513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000752277513 none C[C@@H](C[C@@H](O)c1cccs1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 14, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 7, 7, 11, 17, 17, 17, 38, 38, 38, 38, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 7, 7, 7, 11, 11, 51, 38, 38, 38, 3, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 198 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000752277513 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277513/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277513/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277513 Building ZINC000752277513 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277513' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752277513 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277513/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 201) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H](C[C@@H](O)c1cccs1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000752277513.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752277513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000752277513 none C[C@@H](C[C@@H](O)c1cccs1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 14, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 6, 6, 10, 17, 17, 17, 37, 37, 37, 37, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 6, 6, 6, 10, 10, 51, 37, 37, 37, 2, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 201 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277513/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 202) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H](C[C@@H](O)c1cccs1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000752277513.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752277513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000752277513 none C[C@@H](C[C@@H](O)c1cccs1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 14, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 7, 7, 11, 17, 17, 17, 38, 38, 38, 38, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 7, 7, 7, 11, 11, 51, 38, 38, 38, 3, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 198 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000752277513 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277513/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277513/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277513 Building ZINC000752277514 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277514' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277514 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752277514 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277514/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277514 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/203 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@H](O)c1cccs1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000752277514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752277514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000752277514 none C[C@H](C[C@H](O)c1cccs1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 14, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 7, 7, 11, 17, 17, 17, 38, 38, 38, 38, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 7, 7, 7, 11, 11, 51, 38, 38, 38, 3, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 200 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277514 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277514/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277514 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/204 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/204' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@H](O)c1cccs1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000752277514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752277514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000752277514 none C[C@H](C[C@H](O)c1cccs1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 14, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 6, 6, 10, 16, 16, 16, 36, 36, 36, 36, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 6, 6, 6, 10, 10, 48, 36, 36, 36, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 195 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277514 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000752277514 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277514/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277514/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277514 Building ZINC000752277514 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277514' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277514 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752277514 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277514/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277514 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 203) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H](C[C@H](O)c1cccs1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000752277514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752277514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000752277514 none C[C@H](C[C@H](O)c1cccs1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 14, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 7, 7, 11, 17, 17, 17, 38, 38, 38, 38, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 7, 7, 7, 11, 11, 51, 38, 38, 38, 3, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 200 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277514 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277514/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277514 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 204) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H](C[C@H](O)c1cccs1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000752277514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752277514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000752277514 none C[C@H](C[C@H](O)c1cccs1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 14, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 6, 6, 10, 16, 16, 16, 36, 36, 36, 36, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 6, 6, 6, 10, 10, 48, 36, 36, 36, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 195 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277514 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000752277514 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277514/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277514/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752277514 Building ZINC000752430848 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430848' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430848 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752430848 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430848/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430848 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/205 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)OC) `ZINC000752430848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752430848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000752430848 none CCCCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 19, 17, 8, 3, 8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 8, 16, 16, 16, 19, 19, 19, 19, 19, 19, 19, 18, 19, 18, 18, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430848 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430848/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430848 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/206 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/206' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)OC) `ZINC000752430848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752430848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000752430848 none CCCCC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 14, 7, 2, 7, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 15, 15, 15, 19, 19, 19, 19, 19, 19, 19, 17, 18, 17, 17, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430848 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000752430848 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430848/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430848/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430848 Building ZINC000752430848 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430848' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430848 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752430848 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430848/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430848 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 205) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCCCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)OC) `ZINC000752430848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752430848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000752430848 none CCCCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 19, 17, 8, 3, 8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 8, 16, 16, 16, 19, 19, 19, 19, 19, 19, 19, 18, 19, 18, 18, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430848 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430848/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430848 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 206) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCCCC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)OC) `ZINC000752430848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752430848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000752430848 none CCCCC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 14, 7, 2, 7, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 15, 15, 15, 19, 19, 19, 19, 19, 19, 19, 17, 18, 17, 17, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430848 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000752430848 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430848/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430848/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430848 Building ZINC000752430849 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430849' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430849 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752430849 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430849/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430849 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/207 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)OC) `ZINC000752430849.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752430849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000752430849 none CCCCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 15, 7, 2, 7, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 15, 15, 15, 21, 21, 21, 21, 21, 21, 21, 19, 18, 18, 18, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430849 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430849/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430849 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/208 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/208' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)OC) `ZINC000752430849.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752430849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000752430849 none CCCCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 19, 16, 9, 3, 9, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 9, 17, 17, 17, 19, 19, 19, 19, 19, 19, 19, 19, 18, 18, 18, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 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, 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/83235/xao-8058115.15/working/building/ZINC000752430849 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000752430849 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430849/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430849/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430849 Building ZINC000752430849 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430849' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430849 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752430849 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430849/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430849 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 207) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCCCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)OC) `ZINC000752430849.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752430849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000752430849 none CCCCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 15, 7, 2, 7, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 15, 15, 15, 21, 21, 21, 21, 21, 21, 21, 19, 18, 18, 18, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430849 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430849/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430849 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 208) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCCCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)OC) `ZINC000752430849.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752430849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000752430849 none CCCCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 19, 16, 9, 3, 9, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 9, 17, 17, 17, 19, 19, 19, 19, 19, 19, 19, 19, 18, 18, 18, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 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, 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/83235/xao-8058115.15/working/building/ZINC000752430849 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000752430849 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430849/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430849/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000752430849 Building ZINC000337167222 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167222' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167222 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337167222 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167222/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167222 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/209 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/209' -> `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]2CCCC(F)(F)C2)cn1) `ZINC000337167222.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337167222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337167222 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCCC(F)(F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 15, 15, 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] 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: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 15, 29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167222 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167222/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167222 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/210 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/210' -> `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]2CCCC(F)(F)C2)cn1) `ZINC000337167222.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337167222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167222/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337167222 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCCC(F)(F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 15, 15, 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] 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, 15, 32, 32, 32, 32, 32, 32, 32, 32, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 2, 13, 13, 32, 32, 32, 32, 32, 32, 32, 32, 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: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167222 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337167222 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167222/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167222/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167222 Building ZINC000337167222 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167222' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167222 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337167222 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167222/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167222 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 209) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCCC(F)(F)C2)cn1) `ZINC000337167222.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337167222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337167222 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCCC(F)(F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 15, 15, 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] 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: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 15, 29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167222 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167222/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167222 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 210) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCCC(F)(F)C2)cn1) `ZINC000337167222.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337167222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167222/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337167222 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCCC(F)(F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 15, 15, 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] 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, 15, 32, 32, 32, 32, 32, 32, 32, 32, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 2, 13, 13, 32, 32, 32, 32, 32, 32, 32, 32, 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: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167222 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337167222 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167222/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167222/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167222 Building ZINC000337167223 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167223' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167223 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337167223 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167223/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167223 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/211 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/211' -> `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]2CCCC(F)(F)C2)cn1) `ZINC000337167223.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337167223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337167223 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCCC(F)(F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 15, 15, 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] 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, 15, 33, 33, 33, 33, 33, 33, 33, 33, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 2, 12, 12, 33, 33, 33, 33, 33, 33, 33, 33, 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: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167223 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167223/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167223 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/212 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/212' -> `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]2CCCC(F)(F)C2)cn1) `ZINC000337167223.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337167223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337167223 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCCC(F)(F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 15, 15, 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] 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: [9, 5, 9, 9, 5, 5, 1, 1, 1, 1, 2, 2, 2, 16, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 2, 14, 14, 30, 30, 30, 30, 30, 30, 30, 30, 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: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167223 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337167223 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167223/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167223/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167223 Building ZINC000337167223 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167223' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167223 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337167223 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167223/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167223 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 211) grep: /scratch/xiaobo/83235/xao-8058115.15/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)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCCC(F)(F)C2)cn1) `ZINC000337167223.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337167223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337167223 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCCC(F)(F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 15, 15, 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] 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, 15, 33, 33, 33, 33, 33, 33, 33, 33, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 2, 12, 12, 33, 33, 33, 33, 33, 33, 33, 33, 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: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167223 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167223/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167223 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 212) grep: /scratch/xiaobo/83235/xao-8058115.15/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)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCCC(F)(F)C2)cn1) `ZINC000337167223.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337167223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337167223 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCCC(F)(F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 15, 15, 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] 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: [9, 5, 9, 9, 5, 5, 1, 1, 1, 1, 2, 2, 2, 16, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 2, 14, 14, 30, 30, 30, 30, 30, 30, 30, 30, 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: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167223 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337167223 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167223/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167223/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337167223 Building ZINC000337168113 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337168113' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337168113 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337168113 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337168113/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337168113 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/213 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSCCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000337168113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337168113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337168113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000337168113 none CCSCCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.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', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 20, 18, 11, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 20, 20, 20, 20, 11, 11, 3, 2, 2, 2, 2] 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]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337168113 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337168113/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337168113 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/214 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/214' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSCCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000337168113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337168113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337168113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000337168113 none CCSCCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.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', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 20, 18, 11, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 50, 50, 50, 50, 50, 20, 20, 20, 20, 11, 11, 3, 2, 2, 2, 2] 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]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337168113 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337168113 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337168113/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337168113/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337168113 Building ZINC000337168113 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337168113' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337168113 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337168113 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337168113/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337168113 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 213) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCSCCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000337168113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337168113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337168113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000337168113 none CCSCCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.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', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 20, 18, 11, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 20, 20, 20, 20, 11, 11, 3, 2, 2, 2, 2] 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]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337168113 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337168113/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337168113 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 214) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCSCCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000337168113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337168113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337168113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000337168113 none CCSCCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.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', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 20, 18, 11, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 50, 50, 50, 50, 50, 20, 20, 20, 20, 11, 11, 3, 2, 2, 2, 2] 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]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337168113 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337168113 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337168113/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337168113/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337168113 Building ZINC000927354668 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927354668' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927354668 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927354668 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927354668/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927354668 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/215 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)OC(C)(C)C) `ZINC000927354668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927354668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927354668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000927354668 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 14, 27, 46, 46, 50, 50, 50, 50, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 14, 14, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927354668 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927354668/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927354668 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/216 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/216' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)OC(C)(C)C) `ZINC000927354668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927354668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927354668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000927354668 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 3, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 17, 33, 49, 49, 50, 50, 50, 50, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 17, 17, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927354668 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000927354668 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927354668/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927354668/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927354668 Building ZINC000927354668 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927354668' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927354668 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927354668 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927354668/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927354668 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 215) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)OC(C)(C)C) `ZINC000927354668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927354668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927354668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000927354668 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 14, 27, 46, 46, 50, 50, 50, 50, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 14, 14, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927354668 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927354668/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927354668 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 216) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)OC(C)(C)C) `ZINC000927354668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927354668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927354668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000927354668 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 3, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 17, 33, 49, 49, 50, 50, 50, 50, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 17, 17, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927354668 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000927354668 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927354668/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927354668/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927354668 Building ZINC000337172981 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337172981' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337172981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337172981 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337172981/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337172981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/217 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(C)c(OC)c1) `ZINC000337172981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337172981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337172981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000337172981 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(C)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 1, 12, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 16, 16, 16, 7, 9, 9, 9, 9, 18, 9, 11, 11, 11, 9, 4, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 9, 9, 9, 18, 18, 18, 9] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337172981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337172981/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337172981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/218 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/218' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(C)c(OC)c1) `ZINC000337172981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337172981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337172981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000337172981 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(C)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 1, 12, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 9, 9, 9, 9, 20, 4, 11, 11, 11, 9, 4, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 9, 9, 9, 20, 20, 20, 4] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337172981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337172981 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337172981/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337172981/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337172981 Building ZINC000337172981 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337172981' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337172981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337172981 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337172981/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337172981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 217) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(C)c(OC)c1) `ZINC000337172981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337172981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337172981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000337172981 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(C)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 1, 12, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 16, 16, 16, 7, 9, 9, 9, 9, 18, 9, 11, 11, 11, 9, 4, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 9, 9, 9, 18, 18, 18, 9] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337172981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337172981/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337172981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 218) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(C)c(OC)c1) `ZINC000337172981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337172981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337172981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000337172981 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(C)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 1, 12, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 9, 9, 9, 9, 20, 4, 11, 11, 11, 9, 4, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 9, 9, 9, 20, 20, 20, 4] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337172981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337172981 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337172981/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337172981/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337172981 Building ZINC000337174056 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337174056' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337174056 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337174056 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337174056/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337174056 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/219 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCC1) `ZINC000337174056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337174056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337174056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000337174056 none COCC1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 25, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 44, 44, 44, 50, 50, 50, 50, 50, 14, 14, 2, 3, 3, 3, 3, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337174056 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337174056/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337174056 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/220 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/220' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCC1) `ZINC000337174056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337174056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337174056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000337174056 none COCC1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 25, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 43, 43, 43, 50, 50, 50, 50, 50, 15, 15, 3, 3, 3, 3, 3, 43, 43, 43, 43, 43, 43] 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]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337174056 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337174056 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337174056/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337174056/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337174056 Building ZINC000337174056 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337174056' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337174056 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337174056 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337174056/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337174056 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 219) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COCC1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCC1) `ZINC000337174056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337174056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337174056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000337174056 none COCC1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 25, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 44, 44, 44, 50, 50, 50, 50, 50, 14, 14, 2, 3, 3, 3, 3, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337174056 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337174056/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337174056 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 220) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COCC1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCC1) `ZINC000337174056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337174056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337174056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000337174056 none COCC1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 25, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 43, 43, 43, 50, 50, 50, 50, 50, 15, 15, 3, 3, 3, 3, 3, 43, 43, 43, 43, 43, 43] 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]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337174056 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337174056 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337174056/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337174056/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337174056 Building ZINC000788233295 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788233295' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788233295 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000788233295 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788233295/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788233295 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/221 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(Cl)c1CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000788233295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000788233295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788233295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000788233295 none Cc1nn(C)c(Cl)c1CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'Cl', 'C.2', '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, 8, 8, 5, 1, 16, 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: [31, 31, 31, 31, 31, 31, 31, 17, 6, 2, 6, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31, 17, 17, 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788233295 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788233295/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788233295 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/222 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/222' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(Cl)c1CN(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000788233295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000788233295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788233295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000788233295 none Cc1nn(C)c(Cl)c1CN(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'Cl', 'C.2', '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, 8, 8, 5, 1, 16, 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, 30, 30, 30, 30, 16, 6, 2, 6, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 16, 16, 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: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788233295 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000788233295 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788233295/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788233295/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788233295 Building ZINC000788233295 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788233295' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788233295 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000788233295 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788233295/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788233295 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 221) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(Cl)c1CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000788233295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000788233295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788233295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000788233295 none Cc1nn(C)c(Cl)c1CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'Cl', 'C.2', '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, 8, 8, 5, 1, 16, 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: [31, 31, 31, 31, 31, 31, 31, 17, 6, 2, 6, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31, 17, 17, 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788233295 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788233295/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788233295 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 222) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(Cl)c1CN(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000788233295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000788233295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788233295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000788233295 none Cc1nn(C)c(Cl)c1CN(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'Cl', 'C.2', '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, 8, 8, 5, 1, 16, 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, 30, 30, 30, 30, 16, 6, 2, 6, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 16, 16, 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: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788233295 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000788233295 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788233295/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788233295/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788233295 Building ZINC000428921242 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921242' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921242 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428921242 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921242/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921242 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/223 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)c1ccccc1) `ZINC000428921242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428921242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000428921242 none COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 20, 4, 8, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 18, 18, 8, 18, 18, 20, 20, 20, 4, 8, 8, 18, 18, 8, 18, 18] 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]) total number of confs: 122 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921242 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921242/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921242 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/224 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/224' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)c1ccccc1) `ZINC000428921242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428921242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000428921242 none COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 19, 4, 7, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 7, 15, 15, 7, 15, 15, 19, 19, 19, 4, 8, 8, 15, 15, 7, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 107 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921242 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428921242 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921242/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921242/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921242 Building ZINC000428921242 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921242' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921242 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428921242 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921242/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921242 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 223) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)c1ccccc1) `ZINC000428921242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428921242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000428921242 none COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 20, 4, 8, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 18, 18, 8, 18, 18, 20, 20, 20, 4, 8, 8, 18, 18, 8, 18, 18] 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]) total number of confs: 122 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921242 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921242/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921242 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 224) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)c1ccccc1) `ZINC000428921242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428921242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000428921242 none COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 19, 4, 7, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 7, 15, 15, 7, 15, 15, 19, 19, 19, 4, 8, 8, 15, 15, 7, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 107 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921242 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428921242 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921242/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921242/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921242 Building ZINC000428921243 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921243' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921243 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428921243 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921243/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921243 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/225 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)c1ccccc1) `ZINC000428921243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428921243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000428921243 none COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 19, 4, 7, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 7, 16, 16, 7, 16, 16, 19, 19, 19, 4, 9, 9, 16, 16, 7, 16, 16] 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]) total number of confs: 113 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921243 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921243/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921243 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/226 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/226' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)c1ccccc1) `ZINC000428921243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428921243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000428921243 none COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 20, 4, 8, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 18, 18, 8, 18, 18, 20, 20, 20, 4, 8, 8, 18, 18, 8, 18, 18] 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]) total number of confs: 122 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921243 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428921243 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921243/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921243/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921243 Building ZINC000428921243 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921243' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921243 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428921243 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921243/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921243 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 225) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)c1ccccc1) `ZINC000428921243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428921243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000428921243 none COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 19, 4, 7, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 7, 16, 16, 7, 16, 16, 19, 19, 19, 4, 9, 9, 16, 16, 7, 16, 16] 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]) total number of confs: 113 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921243 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921243/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921243 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 226) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)c1ccccc1) `ZINC000428921243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428921243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000428921243 none COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 20, 4, 8, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 18, 18, 8, 18, 18, 20, 20, 20, 4, 8, 8, 18, 18, 8, 18, 18] 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]) total number of confs: 122 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921243 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428921243 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921243/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921243/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428921243 Building ZINC000866938518 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866938518' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866938518 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000866938518 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866938518/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866938518 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/227 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCCCO)C1CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC000866938518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000866938518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866938518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000866938518 none O=C(N(CCCCO)C1CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 5, 13, 15, 31, 42, 5, 14, 14, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 13, 13, 16, 16, 31, 30, 42, 42, 126, 14, 14, 14, 14, 14, 3, 1, 3] 150 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 364 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866938518 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866938518/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866938518 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/228 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/228' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCCCO)C1CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC000866938518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000866938518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866938518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000866938518 none O=C(N(CCCCO)C1CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 5, 13, 16, 33, 43, 5, 14, 14, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 13, 13, 17, 17, 32, 33, 43, 43, 129, 14, 14, 14, 14, 14, 3, 3, 3] 150 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 375 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866938518 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000866938518 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866938518/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866938518/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866938518 Building ZINC000866938518 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866938518' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866938518 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000866938518 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866938518/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866938518 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 227) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N(CCCCO)C1CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC000866938518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000866938518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866938518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000866938518 none O=C(N(CCCCO)C1CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 5, 13, 15, 31, 42, 5, 14, 14, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 13, 13, 16, 16, 31, 30, 42, 42, 126, 14, 14, 14, 14, 14, 3, 1, 3] 150 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 364 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866938518 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866938518/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866938518 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 228) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N(CCCCO)C1CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC000866938518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000866938518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866938518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000866938518 none O=C(N(CCCCO)C1CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 5, 13, 16, 33, 43, 5, 14, 14, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 13, 13, 17, 17, 32, 33, 43, 43, 129, 14, 14, 14, 14, 14, 3, 3, 3] 150 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 375 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866938518 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000866938518 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866938518/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866938518/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866938518 Building ZINC000927388815 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000927388815 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/229 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS[C@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000927388815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927388815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000927388815 none CS[C@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 7, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 13, 27, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 27, 27, 40, 40, 40, 27, 27, 27, 27, 13, 13, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 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: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/230 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/230' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS[C@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000927388815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927388815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000927388815 none CS[C@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 7, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 27, 27, 27, 27, 27, 14, 27, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 27, 27, 41, 41, 41, 27, 27, 27, 27, 14, 14, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/231 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/231' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS[C@H]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000927388815.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000927388815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000927388815 none CS[C@H]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 7, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 26, 26, 40, 40, 40, 26, 26, 26, 26, 12, 12, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 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: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/232 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/232' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS[C@H]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000927388815.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000927388815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000927388815 none CS[C@H]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 7, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 14, 27, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 27, 27, 40, 40, 40, 27, 27, 27, 27, 14, 14, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000927388815 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 Building ZINC000927388815 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000927388815 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 229) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CS[C@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000927388815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927388815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000927388815 none CS[C@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 7, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 13, 27, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 27, 27, 40, 40, 40, 27, 27, 27, 27, 13, 13, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 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: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 230) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CS[C@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000927388815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927388815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000927388815 none CS[C@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 7, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 27, 27, 27, 27, 27, 14, 27, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 27, 27, 41, 41, 41, 27, 27, 27, 27, 14, 14, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 231) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/231: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS[C@H]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000927388815.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000927388815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000927388815 none CS[C@H]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 7, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 26, 26, 40, 40, 40, 26, 26, 26, 26, 12, 12, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 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: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 232) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/232: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS[C@H]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000927388815.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000927388815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000927388815 none CS[C@H]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 7, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 14, 27, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 27, 27, 40, 40, 40, 27, 27, 27, 27, 14, 14, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000927388815 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 Building ZINC000927388815 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000927388815 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 229) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CS[C@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000927388815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927388815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000927388815 none CS[C@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 7, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 13, 27, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 27, 27, 40, 40, 40, 27, 27, 27, 27, 13, 13, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 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: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 230) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CS[C@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000927388815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927388815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000927388815 none CS[C@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 7, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 27, 27, 27, 27, 27, 14, 27, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 27, 27, 41, 41, 41, 27, 27, 27, 27, 14, 14, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 231) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/231: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS[C@H]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000927388815.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000927388815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000927388815 none CS[C@H]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 7, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 26, 26, 40, 40, 40, 26, 26, 26, 26, 12, 12, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 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: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 232) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/232: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS[C@H]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000927388815.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000927388815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000927388815 none CS[C@H]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 7, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 14, 27, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 27, 27, 40, 40, 40, 27, 27, 27, 27, 14, 14, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000927388815 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 Building ZINC000927388815 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000927388815 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 229) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CS[C@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000927388815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927388815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000927388815 none CS[C@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 7, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 13, 27, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 27, 27, 40, 40, 40, 27, 27, 27, 27, 13, 13, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 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: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 230) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CS[C@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000927388815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927388815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000927388815 none CS[C@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 7, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 27, 27, 27, 27, 27, 14, 27, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 27, 27, 41, 41, 41, 27, 27, 27, 27, 14, 14, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 231) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/231: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS[C@H]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000927388815.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000927388815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000927388815 none CS[C@H]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 7, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 26, 26, 40, 40, 40, 26, 26, 26, 26, 12, 12, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 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: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 232) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/232: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS[C@H]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000927388815.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000927388815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000927388815 none CS[C@H]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 7, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 14, 27, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 27, 27, 40, 40, 40, 27, 27, 27, 27, 14, 14, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000927388815 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927388815 Building ZINC000428938999 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428938999' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428938999 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428938999 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428938999/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428938999 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/233 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(C(=O)Nc2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428938999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428938999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428938999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428938999 none O=C(NC1(C(=O)Nc2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 6, 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: [6, 1, 6, 6, 6, 19, 19, 19, 35, 35, 19, 35, 35, 6, 6, 1, 1, 1, 10, 10, 10, 10, 10, 6, 19, 35, 35, 20, 35, 35, 6, 6, 6, 6, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428938999 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428938999/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428938999 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/234 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/234' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(C(=O)Nc2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428938999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428938999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428938999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428938999 none O=C(NC1(C(=O)Nc2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 6, 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: [6, 1, 6, 6, 6, 19, 19, 19, 34, 34, 27, 34, 34, 6, 6, 1, 1, 1, 10, 10, 10, 10, 10, 6, 19, 34, 34, 34, 34, 34, 6, 6, 6, 6, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428938999 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428938999 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428938999/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428938999/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428938999 Building ZINC000428938999 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428938999' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428938999 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428938999 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428938999/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428938999 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 233) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC1(C(=O)Nc2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428938999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428938999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428938999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428938999 none O=C(NC1(C(=O)Nc2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 6, 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: [6, 1, 6, 6, 6, 19, 19, 19, 35, 35, 19, 35, 35, 6, 6, 1, 1, 1, 10, 10, 10, 10, 10, 6, 19, 35, 35, 20, 35, 35, 6, 6, 6, 6, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428938999 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428938999/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428938999 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 234) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC1(C(=O)Nc2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428938999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428938999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428938999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000428938999 none O=C(NC1(C(=O)Nc2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 6, 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: [6, 1, 6, 6, 6, 19, 19, 19, 34, 34, 27, 34, 34, 6, 6, 1, 1, 1, 10, 10, 10, 10, 10, 6, 19, 34, 34, 34, 34, 34, 6, 6, 6, 6, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428938999 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428938999 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428938999/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428938999/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428938999 Building ZINC000429038698 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038698' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038698 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429038698 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038698/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038698 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/235 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC000429038698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429038698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000429038698 none CO[C@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 35, 18, 35, 17, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 35, 35, 35, 35, 37, 37, 37, 24, 24, 17, 17, 3, 6, 6] 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: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038698 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038698/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038698 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/236 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/236' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC000429038698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429038698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000429038698 none CO[C@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 35, 18, 35, 19, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 35, 35, 35, 35, 36, 36, 36, 27, 27, 19, 19, 3, 7, 7] 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: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038698 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429038698 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038698/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038698/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038698 Building ZINC000429038698 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038698' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038698 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429038698 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038698/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038698 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 235) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CO[C@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC000429038698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429038698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000429038698 none CO[C@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 35, 18, 35, 17, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 35, 35, 35, 35, 37, 37, 37, 24, 24, 17, 17, 3, 6, 6] 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: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038698 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038698/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038698 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 236) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CO[C@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC000429038698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429038698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000429038698 none CO[C@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 35, 18, 35, 19, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 35, 35, 35, 35, 36, 36, 36, 27, 27, 19, 19, 3, 7, 7] 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: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038698 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429038698 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038698/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038698/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038698 Building ZINC000429038701 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038701' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038701 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429038701 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038701/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038701 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/237 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC000429038701.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429038701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000429038701 none CO[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 35, 18, 35, 19, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 35, 35, 35, 35, 36, 36, 36, 27, 27, 19, 19, 3, 7, 7] 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: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038701 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038701/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038701 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/238 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/238' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC000429038701.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429038701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038701/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000429038701 none CO[C@@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 35, 18, 35, 17, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 35, 35, 35, 35, 37, 37, 37, 24, 24, 17, 17, 3, 6, 6] 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: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038701 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429038701 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038701/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038701/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038701 Building ZINC000429038701 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038701' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038701 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429038701 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038701/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038701 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 237) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CO[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC000429038701.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429038701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000429038701 none CO[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 35, 18, 35, 19, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 35, 35, 35, 35, 36, 36, 36, 27, 27, 19, 19, 3, 7, 7] 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: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038701 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038701/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038701 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 238) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CO[C@@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC000429038701.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429038701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038701/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000429038701 none CO[C@@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 35, 18, 35, 17, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 35, 35, 35, 35, 37, 37, 37, 24, 24, 17, 17, 3, 6, 6] 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: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038701 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429038701 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038701/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038701/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429038701 Building ZINC000862394493 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394493' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394493 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000862394493 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394493/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394493 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/239 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@H]1CCCOC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000862394493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000862394493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000862394493 none O=C(NCC[C@H]1CCCOC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 14, 32, 41, 41, 41, 41, 41, 41, 1, 1, 1, 7, 7, 7, 7, 7, 2, 14, 14, 23, 23, 41, 41, 41, 41, 41, 41, 41, 41, 7, 7] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394493 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394493/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394493 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/240 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/240' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@H]1CCCOC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000862394493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000862394493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000862394493 none O=C(NCC[C@H]1CCCOC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 14, 29, 38, 38, 38, 38, 38, 38, 1, 1, 1, 8, 8, 8, 8, 8, 2, 14, 14, 20, 20, 38, 38, 38, 38, 38, 38, 38, 38, 8, 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: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394493 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000862394493 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394493/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394493/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394493 Building ZINC000862394493 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394493' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394493 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000862394493 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394493/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394493 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 239) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NCC[C@H]1CCCOC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000862394493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000862394493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000862394493 none O=C(NCC[C@H]1CCCOC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 14, 32, 41, 41, 41, 41, 41, 41, 1, 1, 1, 7, 7, 7, 7, 7, 2, 14, 14, 23, 23, 41, 41, 41, 41, 41, 41, 41, 41, 7, 7] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394493 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394493/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394493 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 240) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NCC[C@H]1CCCOC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000862394493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000862394493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000862394493 none O=C(NCC[C@H]1CCCOC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 14, 29, 38, 38, 38, 38, 38, 38, 1, 1, 1, 8, 8, 8, 8, 8, 2, 14, 14, 20, 20, 38, 38, 38, 38, 38, 38, 38, 38, 8, 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: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394493 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000862394493 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394493/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394493/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394493 Building ZINC000862394495 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394495' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394495 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000862394495 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394495/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394495 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/241 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@@H]1CCCOC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000862394495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000862394495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000862394495 none O=C(NCC[C@@H]1CCCOC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 14, 24, 35, 35, 35, 35, 35, 35, 1, 1, 1, 8, 8, 8, 8, 8, 2, 14, 14, 24, 24, 35, 35, 35, 35, 35, 35, 35, 35, 8, 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: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394495 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394495/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394495 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/242 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/242' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@@H]1CCCOC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000862394495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000862394495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000862394495 none O=C(NCC[C@@H]1CCCOC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 15, 24, 36, 36, 36, 36, 36, 36, 1, 1, 1, 8, 8, 8, 8, 8, 2, 15, 15, 24, 24, 36, 36, 36, 36, 36, 36, 36, 36, 8, 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: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394495 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000862394495 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394495/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394495/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394495 Building ZINC000862394495 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394495' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394495 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000862394495 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394495/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394495 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 241) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NCC[C@@H]1CCCOC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000862394495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000862394495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000862394495 none O=C(NCC[C@@H]1CCCOC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 14, 24, 35, 35, 35, 35, 35, 35, 1, 1, 1, 8, 8, 8, 8, 8, 2, 14, 14, 24, 24, 35, 35, 35, 35, 35, 35, 35, 35, 8, 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: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394495 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394495/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394495 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 242) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NCC[C@@H]1CCCOC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000862394495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000862394495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000862394495 none O=C(NCC[C@@H]1CCCOC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 15, 24, 36, 36, 36, 36, 36, 36, 1, 1, 1, 8, 8, 8, 8, 8, 2, 15, 15, 24, 24, 36, 36, 36, 36, 36, 36, 36, 36, 8, 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: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394495 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000862394495 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394495/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394495/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862394495 Building ZINC000866134566 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866134566' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866134566 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000866134566 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866134566/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866134566 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/243 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(C(F)(F)F)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CCO1) `ZINC000866134566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000866134566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866134566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000866134566 none C[C@@]1(C(F)(F)F)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 15, 15, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 7, 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, 3, 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: [24, 24, 24, 24, 24, 24, 24, 10, 2, 16, 1, 1, 1, 3, 3, 1, 1, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 3, 3, 24, 24, 24, 24] 26 rigid atoms, others: [10, 11, 12] set([0, 1, 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, 31, 32, 33, 34]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866134566 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866134566/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866134566 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/244 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/244' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(C(F)(F)F)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CCO1) `ZINC000866134566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000866134566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866134566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000866134566 none C[C@@]1(C(F)(F)F)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 15, 15, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 7, 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, 3, 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: [28, 28, 28, 28, 28, 28, 28, 10, 2, 18, 1, 1, 1, 5, 5, 1, 5, 5, 5, 28, 28, 28, 28, 28, 28, 28, 28, 5, 5, 5, 5, 28, 28, 28, 28] 31 rigid atoms, others: [10, 11, 12] set([0, 1, 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, 31, 32, 33, 34]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866134566 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000866134566 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866134566/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866134566/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866134566 Building ZINC000866134566 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866134566' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866134566 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000866134566 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866134566/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866134566 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 243) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@]1(C(F)(F)F)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CCO1) `ZINC000866134566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000866134566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866134566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000866134566 none C[C@@]1(C(F)(F)F)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 15, 15, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 7, 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, 3, 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: [24, 24, 24, 24, 24, 24, 24, 10, 2, 16, 1, 1, 1, 3, 3, 1, 1, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 3, 3, 24, 24, 24, 24] 26 rigid atoms, others: [10, 11, 12] set([0, 1, 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, 31, 32, 33, 34]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866134566 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866134566/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866134566 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 244) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@]1(C(F)(F)F)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CCO1) `ZINC000866134566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000866134566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866134566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000866134566 none C[C@@]1(C(F)(F)F)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 15, 15, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 7, 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, 3, 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: [28, 28, 28, 28, 28, 28, 28, 10, 2, 18, 1, 1, 1, 5, 5, 1, 5, 5, 5, 28, 28, 28, 28, 28, 28, 28, 28, 5, 5, 5, 5, 28, 28, 28, 28] 31 rigid atoms, others: [10, 11, 12] set([0, 1, 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, 31, 32, 33, 34]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866134566 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000866134566 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866134566/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866134566/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000866134566 Building ZINC000159726807 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159726807' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159726807 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000159726807 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159726807/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159726807 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/245 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1CC1CC1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000159726807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000159726807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159726807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000159726807 none O=C(Nc1ccnn1CC1CC1)[C@]([O-])([SiH3])c1ccc(Br)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.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, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 8, 15, 15, 15, 15, 15, 31, 49, 49, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 15, 15, 31, 31, 49, 49, 49, 49, 49, 3, 3, 3, 3] 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: 192 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159726807 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159726807/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159726807 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/246 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/246' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1CC1CC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000159726807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000159726807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159726807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000159726807 none O=C(Nc1ccnn1CC1CC1)[C@@]([O-])([SiH3])c1ccc(Br)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.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, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 8, 15, 15, 15, 15, 15, 32, 47, 47, 1, 1, 1, 3, 3, 3, 3, 3, 3, 8, 15, 15, 32, 32, 47, 47, 47, 47, 47, 3, 3, 3, 3] 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: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159726807 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000159726807 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159726807/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159726807/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159726807 Building ZINC000159726807 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159726807' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159726807 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000159726807 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159726807/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159726807 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 245) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(Nc1ccnn1CC1CC1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000159726807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000159726807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159726807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000159726807 none O=C(Nc1ccnn1CC1CC1)[C@]([O-])([SiH3])c1ccc(Br)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.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, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 8, 15, 15, 15, 15, 15, 31, 49, 49, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 15, 15, 31, 31, 49, 49, 49, 49, 49, 3, 3, 3, 3] 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: 192 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159726807 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159726807/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159726807 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 246) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(Nc1ccnn1CC1CC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000159726807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000159726807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159726807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000159726807 none O=C(Nc1ccnn1CC1CC1)[C@@]([O-])([SiH3])c1ccc(Br)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.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, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 8, 15, 15, 15, 15, 15, 32, 47, 47, 1, 1, 1, 3, 3, 3, 3, 3, 3, 8, 15, 15, 32, 32, 47, 47, 47, 47, 47, 3, 3, 3, 3] 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: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159726807 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000159726807 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159726807/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159726807/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159726807 Building ZINC000429090849 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429090849' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429090849 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429090849 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429090849/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429090849 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/247 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCC1) `ZINC000429090849.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429090849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429090849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000429090849 none CCOC(=O)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', '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, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 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, 3, 7, 5, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 16, 20, 11, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 12, 17, 17, 17, 23, 23, 23, 23, 23, 16, 16, 7, 7, 17, 17, 17, 17, 17, 17, 17] 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]) total number of confs: 108 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429090849 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429090849/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429090849 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/248 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/248' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCC1) `ZINC000429090849.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429090849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429090849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000429090849 none CCOC(=O)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', '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, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 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, 3, 7, 5, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 19, 19, 15, 19, 12, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 13, 21, 21, 21, 25, 25, 25, 25, 25, 15, 15, 6, 6, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429090849 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429090849 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429090849/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429090849/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429090849 Building ZINC000429090849 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429090849' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429090849 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429090849 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429090849/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429090849 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 247) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCOC(=O)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCC1) `ZINC000429090849.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429090849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429090849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000429090849 none CCOC(=O)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', '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, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 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, 3, 7, 5, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 16, 20, 11, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 12, 17, 17, 17, 23, 23, 23, 23, 23, 16, 16, 7, 7, 17, 17, 17, 17, 17, 17, 17] 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]) total number of confs: 108 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429090849 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429090849/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429090849 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 248) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCOC(=O)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCC1) `ZINC000429090849.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429090849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429090849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000429090849 none CCOC(=O)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', '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, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 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, 3, 7, 5, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 19, 19, 15, 19, 12, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 13, 21, 21, 21, 25, 25, 25, 25, 25, 15, 15, 6, 6, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429090849 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429090849 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429090849/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429090849/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429090849 Building ZINC000429091788 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429091788' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429091788 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429091788 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429091788/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429091788 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/249 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1CCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429091788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429091788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429091788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000429091788 none Cc1nn(C)c(C)c1CCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 44, 26, 20, 13, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 44, 44, 44, 44, 44, 44, 44, 44, 44, 26, 26, 26, 26, 13, 13, 2, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429091788 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429091788/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429091788 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/250 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/250' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1CCCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429091788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429091788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429091788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000429091788 none Cc1nn(C)c(C)c1CCCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 44, 26, 21, 13, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 44, 44, 44, 44, 44, 44, 44, 44, 44, 26, 26, 26, 26, 13, 13, 2, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429091788 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429091788 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429091788/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429091788/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429091788 Building ZINC000429091788 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429091788' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429091788 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429091788 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429091788/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429091788 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 249) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(C)c1CCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429091788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429091788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429091788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000429091788 none Cc1nn(C)c(C)c1CCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 44, 26, 20, 13, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 44, 44, 44, 44, 44, 44, 44, 44, 44, 26, 26, 26, 26, 13, 13, 2, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429091788 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429091788/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429091788 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 250) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(C)c1CCCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429091788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429091788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429091788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000429091788 none Cc1nn(C)c(C)c1CCCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 44, 26, 21, 13, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 44, 44, 44, 44, 44, 44, 44, 44, 44, 26, 26, 26, 26, 13, 13, 2, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429091788 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429091788 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429091788/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429091788/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429091788 Building ZINC000337191748 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337191748' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337191748 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337191748 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337191748/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337191748 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/251 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(F)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1OC) `ZINC000337191748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337191748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337191748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000337191748 none COc1cc(F)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 7, 7, 7, 7, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 7, 7, 7, 15, 14, 14, 14, 7, 4, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 7, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337191748 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337191748/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337191748 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/252 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/252' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(F)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1OC) `ZINC000337191748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337191748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337191748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000337191748 none COc1cc(F)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 17, 17, 17, 7, 6, 6, 6, 14, 13, 13, 13, 6, 3, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 6, 14, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337191748 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337191748 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337191748/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337191748/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337191748 Building ZINC000337191748 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337191748' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337191748 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337191748 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337191748/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337191748 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 251) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1cc(F)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1OC) `ZINC000337191748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337191748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337191748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000337191748 none COc1cc(F)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 7, 7, 7, 7, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 7, 7, 7, 15, 14, 14, 14, 7, 4, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 7, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337191748 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337191748/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337191748 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 252) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1cc(F)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1OC) `ZINC000337191748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337191748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337191748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000337191748 none COc1cc(F)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 17, 17, 17, 7, 6, 6, 6, 14, 13, 13, 13, 6, 3, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 6, 14, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337191748 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337191748 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337191748/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337191748/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337191748 Building ZINC000527613656 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527613656' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527613656 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000527613656 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527613656/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527613656 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/253 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ncc2c(n1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C2) `ZINC000527613656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000527613656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527613656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000527613656 none CC(C)c1ncc2c(n1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 27, 27, 27, 27, 27, 27, 27, 27, 9, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 3, 3, 3, 3, 27, 27] 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: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527613656 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527613656/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527613656 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/254 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/254' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ncc2c(n1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C2) `ZINC000527613656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000527613656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527613656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000527613656 none CC(C)c1ncc2c(n1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 27, 27, 27, 27, 27, 27, 27, 27, 9, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 3, 3, 3, 3, 27, 27] 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: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527613656 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000527613656 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527613656/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527613656/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527613656 Building ZINC000527613656 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527613656' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527613656 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000527613656 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527613656/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527613656 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 253) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)c1ncc2c(n1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C2) `ZINC000527613656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000527613656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527613656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000527613656 none CC(C)c1ncc2c(n1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 27, 27, 27, 27, 27, 27, 27, 27, 9, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 3, 3, 3, 3, 27, 27] 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: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527613656 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527613656/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527613656 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 254) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)c1ncc2c(n1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C2) `ZINC000527613656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000527613656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527613656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000527613656 none CC(C)c1ncc2c(n1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 27, 27, 27, 27, 27, 27, 27, 27, 9, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 3, 3, 3, 3, 27, 27] 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: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527613656 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000527613656 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527613656/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527613656/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527613656 Building ZINC000429223964 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429223964' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429223964 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429223964 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429223964/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429223964 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/255 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc2c1CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CC2) `ZINC000429223964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429223964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429223964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000429223964 none Cc1cccc2c1CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 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] 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] 0 hydrogens 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, 5, 1, 9, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 19, 19, 19, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429223964 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429223964/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429223964 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/256 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/256' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc2c1CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CC2) `ZINC000429223964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429223964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429223964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000429223964 none Cc1cccc2c1CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 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] 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] 0 hydrogens 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, 5, 1, 9, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 19, 19, 19, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429223964 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429223964 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429223964/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429223964/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429223964 Building ZINC000429223964 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429223964' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429223964 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429223964 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429223964/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429223964 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 255) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1cccc2c1CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CC2) `ZINC000429223964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429223964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429223964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000429223964 none Cc1cccc2c1CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 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] 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] 0 hydrogens 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, 5, 1, 9, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 19, 19, 19, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429223964 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429223964/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429223964 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 256) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1cccc2c1CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CC2) `ZINC000429223964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429223964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429223964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000429223964 none Cc1cccc2c1CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 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] 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] 0 hydrogens 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, 5, 1, 9, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 19, 19, 19, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429223964 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429223964 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429223964/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429223964/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429223964 Building ZINC000527621704 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527621704' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527621704 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000527621704 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527621704/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527621704 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/257 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ncc2c(n1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)C2) `ZINC000527621704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000527621704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527621704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000527621704 none CC(C)c1ncc2c(n1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 10, 32, 10, 10, 10, 10, 10, 10, 10, 10, 4, 2, 8, 1, 1, 1, 6, 6, 11, 11, 6, 11, 11, 11, 10, 32, 32, 32, 32, 32, 32, 32, 10, 10, 10, 10, 10, 6, 11, 11, 11, 11, 11, 11, 11, 11, 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, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527621704 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527621704/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527621704 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/258 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/258' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ncc2c(n1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)C2) `ZINC000527621704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000527621704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527621704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000527621704 none CC(C)c1ncc2c(n1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 32, 11, 11, 11, 11, 11, 11, 11, 11, 4, 2, 8, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 11, 32, 32, 32, 32, 32, 32, 32, 11, 11, 11, 11, 11, 6, 10, 10, 10, 10, 10, 10, 10, 10, 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, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527621704 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000527621704 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527621704/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527621704/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527621704 Building ZINC000527621704 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527621704' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527621704 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000527621704 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527621704/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527621704 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 257) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)c1ncc2c(n1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)C2) `ZINC000527621704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000527621704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527621704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000527621704 none CC(C)c1ncc2c(n1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 10, 32, 10, 10, 10, 10, 10, 10, 10, 10, 4, 2, 8, 1, 1, 1, 6, 6, 11, 11, 6, 11, 11, 11, 10, 32, 32, 32, 32, 32, 32, 32, 10, 10, 10, 10, 10, 6, 11, 11, 11, 11, 11, 11, 11, 11, 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, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527621704 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527621704/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527621704 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 258) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)c1ncc2c(n1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)C2) `ZINC000527621704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000527621704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527621704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000527621704 none CC(C)c1ncc2c(n1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 32, 11, 11, 11, 11, 11, 11, 11, 11, 4, 2, 8, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 11, 32, 32, 32, 32, 32, 32, 32, 11, 11, 11, 11, 11, 6, 10, 10, 10, 10, 10, 10, 10, 10, 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, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527621704 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000527621704 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527621704/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527621704/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527621704 Building ZINC000527626211 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527626211' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527626211 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000527626211 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527626211/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527626211 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/259 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCc2nc(C(C)C)ncc2C1) `ZINC000527626211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000527626211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527626211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000527626211 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCc2nc(C(C)C)ncc2C1 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.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 5, 5, 5, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 7, 13, 22, 22, 22, 22, 22, 22, 47, 47, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22, 47, 47, 47, 47, 47, 47, 47, 22, 22, 22] 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527626211 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527626211/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527626211 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/260 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/260' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCc2nc(C(C)C)ncc2C1) `ZINC000527626211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000527626211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527626211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000527626211 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCc2nc(C(C)C)ncc2C1 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.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 5, 5, 5, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 7, 13, 22, 22, 22, 22, 22, 22, 47, 47, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22, 47, 47, 47, 47, 47, 47, 47, 22, 22, 22] 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527626211 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000527626211 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527626211/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527626211/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527626211 Building ZINC000527626211 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527626211' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527626211 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000527626211 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527626211/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527626211 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 259) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCc2nc(C(C)C)ncc2C1) `ZINC000527626211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000527626211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527626211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000527626211 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCc2nc(C(C)C)ncc2C1 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.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 5, 5, 5, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 7, 13, 22, 22, 22, 22, 22, 22, 47, 47, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22, 47, 47, 47, 47, 47, 47, 47, 22, 22, 22] 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527626211 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527626211/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527626211 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 260) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCc2nc(C(C)C)ncc2C1) `ZINC000527626211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000527626211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527626211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000527626211 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCc2nc(C(C)C)ncc2C1 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.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 5, 5, 5, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 7, 13, 22, 22, 22, 22, 22, 22, 47, 47, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22, 47, 47, 47, 47, 47, 47, 47, 22, 22, 22] 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527626211 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000527626211 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527626211/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527626211/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000527626211 Building ZINC000013685543 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000013685543' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000013685543 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000013685543 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000013685543/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000013685543 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/261 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccccc32)cc1OC) `ZINC000013685543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000013685543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000013685543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000013685543 none COc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 26, 26, 26, 26, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 26, 26, 26, 44, 44, 44, 44, 26, 26, 10, 10, 2, 3, 3, 3, 3, 3, 26, 44, 44, 44] 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000013685543 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000013685543/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000013685543 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/262 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/262' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccccc32)cc1OC) `ZINC000013685543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000013685543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000013685543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000013685543 none COc1ccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 27, 27, 27, 44, 44, 44, 44, 27, 27, 10, 10, 2, 3, 3, 3, 3, 3, 27, 44, 44, 44] 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000013685543 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000013685543 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000013685543/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000013685543/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000013685543 Building ZINC000013685543 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000013685543' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000013685543 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000013685543 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000013685543/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000013685543 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 261) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccccc32)cc1OC) `ZINC000013685543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000013685543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000013685543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000013685543 none COc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 26, 26, 26, 26, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 26, 26, 26, 44, 44, 44, 44, 26, 26, 10, 10, 2, 3, 3, 3, 3, 3, 26, 44, 44, 44] 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000013685543 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000013685543/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000013685543 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 262) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccccc32)cc1OC) `ZINC000013685543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000013685543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000013685543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000013685543 none COc1ccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 27, 27, 27, 44, 44, 44, 44, 27, 27, 10, 10, 2, 3, 3, 3, 3, 3, 27, 44, 44, 44] 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000013685543 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000013685543 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000013685543/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000013685543/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000013685543 Building ZINC000337213563 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337213563' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337213563 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337213563 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337213563/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337213563 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/263 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1(C(F)F)CC1) `ZINC000337213563.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337213563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337213563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000337213563 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1(C(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 10, 10, 3, 3, 1, 1, 1, 1, 7, 7, 7, 13, 36, 36, 13, 13, 3, 3, 3, 10, 10, 6, 10, 10, 3, 3, 3, 7, 36, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 172 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337213563 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337213563/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337213563 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/264 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/264' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1(C(F)F)CC1) `ZINC000337213563.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337213563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337213563/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000337213563 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1(C(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 1, 1, 1, 1, 8, 8, 8, 14, 38, 38, 14, 14, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 4, 8, 38, 14, 14, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 178 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337213563 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337213563 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337213563/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337213563/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337213563 Building ZINC000337213563 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337213563' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337213563 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337213563 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337213563/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337213563 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 263) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1(C(F)F)CC1) `ZINC000337213563.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337213563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337213563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000337213563 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1(C(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 10, 10, 3, 3, 1, 1, 1, 1, 7, 7, 7, 13, 36, 36, 13, 13, 3, 3, 3, 10, 10, 6, 10, 10, 3, 3, 3, 7, 36, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 172 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337213563 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337213563/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337213563 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 264) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1(C(F)F)CC1) `ZINC000337213563.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337213563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337213563/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000337213563 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1(C(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 1, 1, 1, 1, 8, 8, 8, 14, 38, 38, 14, 14, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 4, 8, 38, 14, 14, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 178 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337213563 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337213563 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337213563/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337213563/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337213563 Building ZINC000429488310 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429488310' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429488310 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429488310 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429488310/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429488310 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/265 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)sc1C1CC1) `ZINC000429488310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429488310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429488310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000429488310 none COC(=O)c1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)sc1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.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', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 1, 5, 5, 5, 7, 7, 7, 6, 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] 0 hydrogens 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, 8, 47, 8, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 8, 8, 23, 23, 47, 47, 47, 4, 3, 3, 3, 3, 23, 23, 23, 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, 35, 36]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429488310 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429488310/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429488310 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/266 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/266' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)sc1C1CC1) `ZINC000429488310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429488310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429488310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000429488310 none COC(=O)c1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)sc1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.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', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 1, 5, 5, 5, 7, 7, 7, 6, 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] 0 hydrogens 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, 8, 45, 8, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 8, 8, 23, 23, 45, 45, 45, 4, 3, 3, 3, 3, 23, 23, 23, 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, 35, 36]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429488310 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429488310 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429488310/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429488310/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429488310 Building ZINC000429488310 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429488310' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429488310 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429488310 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429488310/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429488310 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 265) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC(=O)c1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)sc1C1CC1) `ZINC000429488310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429488310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429488310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000429488310 none COC(=O)c1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)sc1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.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', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 1, 5, 5, 5, 7, 7, 7, 6, 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] 0 hydrogens 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, 8, 47, 8, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 8, 8, 23, 23, 47, 47, 47, 4, 3, 3, 3, 3, 23, 23, 23, 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, 35, 36]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429488310 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429488310/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429488310 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 266) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC(=O)c1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)sc1C1CC1) `ZINC000429488310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429488310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429488310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000429488310 none COC(=O)c1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)sc1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.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', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 1, 5, 5, 5, 7, 7, 7, 6, 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] 0 hydrogens 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, 8, 45, 8, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 8, 8, 23, 23, 45, 45, 45, 4, 3, 3, 3, 3, 23, 23, 23, 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, 35, 36]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429488310 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429488310 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429488310/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429488310/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429488310 Building ZINC000429650347 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429650347' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429650347 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429650347 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429650347/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429650347 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/267 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1noc(CCCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)n1) `ZINC000429650347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429650347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429650347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000429650347 none CC(C)c1noc(CCCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 14, 10, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 12, 12, 10, 10, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429650347 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429650347/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429650347 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/268 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/268' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1noc(CCCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)n1) `ZINC000429650347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429650347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429650347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000429650347 none CC(C)c1noc(CCCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 14, 10, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 12, 12, 10, 10, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429650347 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429650347 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429650347/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429650347/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429650347 Building ZINC000429650347 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429650347' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429650347 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429650347 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429650347/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429650347 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 267) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)c1noc(CCCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)n1) `ZINC000429650347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429650347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429650347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000429650347 none CC(C)c1noc(CCCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 14, 10, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 12, 12, 10, 10, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429650347 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429650347/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429650347 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 268) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)c1noc(CCCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)n1) `ZINC000429650347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429650347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429650347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000429650347 none CC(C)c1noc(CCCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 14, 10, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 12, 12, 10, 10, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429650347 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429650347 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429650347/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429650347/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429650347 Building ZINC000429642728 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000429642728 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/269 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1) `ZINC000429642728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429642728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429642728 none CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 19, 16, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 25, 38, 38, 38, 38, 38, 25, 25, 25, 19, 19, 16, 16, 3, 7, 7, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38] 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]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/270 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/270' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1) `ZINC000429642728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429642728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429642728 none CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 19, 16, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 25, 38, 38, 38, 38, 38, 25, 25, 25, 19, 19, 16, 16, 3, 7, 7, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38] 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]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/271 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/271' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1) `ZINC000429642728.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000429642728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429642728 none CN(CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 20, 17, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 26, 40, 40, 40, 40, 40, 26, 26, 26, 20, 20, 17, 17, 3, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 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]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/272 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/272' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1) `ZINC000429642728.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000429642728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429642728 none CN(CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 20, 17, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 26, 40, 40, 40, 40, 40, 26, 26, 26, 20, 20, 17, 17, 3, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 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]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429642728 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 Building ZINC000429642728 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000429642728 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 269) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1) `ZINC000429642728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429642728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429642728 none CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 19, 16, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 25, 38, 38, 38, 38, 38, 25, 25, 25, 19, 19, 16, 16, 3, 7, 7, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38] 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]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 270) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1) `ZINC000429642728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429642728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429642728 none CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 19, 16, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 25, 38, 38, 38, 38, 38, 25, 25, 25, 19, 19, 16, 16, 3, 7, 7, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38] 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]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 271) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/271: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1) `ZINC000429642728.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000429642728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429642728 none CN(CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 20, 17, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 26, 40, 40, 40, 40, 40, 26, 26, 26, 20, 20, 17, 17, 3, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 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]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 272) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/272: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1) `ZINC000429642728.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000429642728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429642728 none CN(CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 20, 17, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 26, 40, 40, 40, 40, 40, 26, 26, 26, 20, 20, 17, 17, 3, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 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]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429642728 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 Building ZINC000429642728 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000429642728 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 269) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1) `ZINC000429642728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429642728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429642728 none CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 19, 16, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 25, 38, 38, 38, 38, 38, 25, 25, 25, 19, 19, 16, 16, 3, 7, 7, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38] 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]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 270) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1) `ZINC000429642728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429642728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429642728 none CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 19, 16, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 25, 38, 38, 38, 38, 38, 25, 25, 25, 19, 19, 16, 16, 3, 7, 7, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38] 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]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 271) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/271: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1) `ZINC000429642728.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000429642728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429642728 none CN(CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 20, 17, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 26, 40, 40, 40, 40, 40, 26, 26, 26, 20, 20, 17, 17, 3, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 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]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 272) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/272: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1) `ZINC000429642728.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000429642728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429642728 none CN(CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 20, 17, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 26, 40, 40, 40, 40, 40, 26, 26, 26, 20, 20, 17, 17, 3, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 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]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429642728 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 Building ZINC000429642728 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000429642728 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 269) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1) `ZINC000429642728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429642728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429642728 none CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 19, 16, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 25, 38, 38, 38, 38, 38, 25, 25, 25, 19, 19, 16, 16, 3, 7, 7, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38] 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]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 270) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1) `ZINC000429642728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429642728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429642728 none CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 19, 16, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 25, 38, 38, 38, 38, 38, 25, 25, 25, 19, 19, 16, 16, 3, 7, 7, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38] 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]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 271) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/271: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1) `ZINC000429642728.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000429642728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429642728 none CN(CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 20, 17, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 26, 40, 40, 40, 40, 40, 26, 26, 26, 20, 20, 17, 17, 3, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 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]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 272) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/272: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1) `ZINC000429642728.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000429642728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429642728 none CN(CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 20, 17, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 26, 40, 40, 40, 40, 40, 26, 26, 26, 20, 20, 17, 17, 3, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 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]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429642728 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429642728 Building ZINC000429663173 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000429663173 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/273 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429663173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429663173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429663173 none CCC[N@]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 44, 39, 39, 39, 39, 23, 39, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 39, 39, 48, 48, 48, 48, 48, 44, 44, 39, 39, 39, 39, 13, 13, 2, 4, 4, 39, 39, 39, 39] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/274 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/274' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429663173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429663173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429663173 none CCC[N@]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 44, 39, 39, 39, 39, 22, 39, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 39, 39, 48, 48, 48, 48, 48, 44, 44, 39, 39, 39, 39, 13, 13, 2, 4, 4, 39, 39, 39, 39] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/275 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/275' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429663173.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000429663173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429663173 none CCC[N@]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 42, 37, 37, 37, 37, 22, 37, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 37, 37, 47, 47, 47, 47, 47, 42, 42, 37, 37, 37, 37, 12, 12, 2, 5, 5, 37, 37, 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, 41]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/276 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/276' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429663173.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000429663173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429663173 none CCC[N@]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 42, 38, 38, 38, 38, 23, 38, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 38, 38, 47, 47, 47, 47, 47, 42, 42, 38, 38, 38, 38, 13, 13, 2, 5, 5, 38, 38, 38, 38] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429663173 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 Building ZINC000429663173 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000429663173 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 273) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCC[N@]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429663173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429663173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429663173 none CCC[N@]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 44, 39, 39, 39, 39, 23, 39, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 39, 39, 48, 48, 48, 48, 48, 44, 44, 39, 39, 39, 39, 13, 13, 2, 4, 4, 39, 39, 39, 39] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 274) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCC[N@]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429663173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429663173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429663173 none CCC[N@]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 44, 39, 39, 39, 39, 22, 39, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 39, 39, 48, 48, 48, 48, 48, 44, 44, 39, 39, 39, 39, 13, 13, 2, 4, 4, 39, 39, 39, 39] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 275) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/275: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429663173.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000429663173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429663173 none CCC[N@]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 42, 37, 37, 37, 37, 22, 37, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 37, 37, 47, 47, 47, 47, 47, 42, 42, 37, 37, 37, 37, 12, 12, 2, 5, 5, 37, 37, 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, 41]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 276) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/276: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429663173.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000429663173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429663173 none CCC[N@]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 42, 38, 38, 38, 38, 23, 38, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 38, 38, 47, 47, 47, 47, 47, 42, 42, 38, 38, 38, 38, 13, 13, 2, 5, 5, 38, 38, 38, 38] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429663173 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 Building ZINC000429663173 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000429663173 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 273) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCC[N@]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429663173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429663173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429663173 none CCC[N@]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 44, 39, 39, 39, 39, 23, 39, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 39, 39, 48, 48, 48, 48, 48, 44, 44, 39, 39, 39, 39, 13, 13, 2, 4, 4, 39, 39, 39, 39] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 274) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCC[N@]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429663173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429663173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429663173 none CCC[N@]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 44, 39, 39, 39, 39, 22, 39, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 39, 39, 48, 48, 48, 48, 48, 44, 44, 39, 39, 39, 39, 13, 13, 2, 4, 4, 39, 39, 39, 39] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 275) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/275: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429663173.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000429663173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429663173 none CCC[N@]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 42, 37, 37, 37, 37, 22, 37, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 37, 37, 47, 47, 47, 47, 47, 42, 42, 37, 37, 37, 37, 12, 12, 2, 5, 5, 37, 37, 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, 41]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 276) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/276: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429663173.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000429663173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429663173 none CCC[N@]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 42, 38, 38, 38, 38, 23, 38, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 38, 38, 47, 47, 47, 47, 47, 42, 42, 38, 38, 38, 38, 13, 13, 2, 5, 5, 38, 38, 38, 38] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429663173 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 Building ZINC000429663173 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000429663173 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 273) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCC[N@]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429663173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429663173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429663173 none CCC[N@]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 44, 39, 39, 39, 39, 23, 39, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 39, 39, 48, 48, 48, 48, 48, 44, 44, 39, 39, 39, 39, 13, 13, 2, 4, 4, 39, 39, 39, 39] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 274) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCC[N@]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429663173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429663173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429663173 none CCC[N@]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 44, 39, 39, 39, 39, 22, 39, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 39, 39, 48, 48, 48, 48, 48, 44, 44, 39, 39, 39, 39, 13, 13, 2, 4, 4, 39, 39, 39, 39] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 275) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/275: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429663173.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000429663173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429663173 none CCC[N@]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 42, 37, 37, 37, 37, 22, 37, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 37, 37, 47, 47, 47, 47, 47, 42, 42, 37, 37, 37, 37, 12, 12, 2, 5, 5, 37, 37, 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, 41]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 276) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/276: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429663173.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000429663173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429663173 none CCC[N@]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 42, 38, 38, 38, 38, 23, 38, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 38, 38, 47, 47, 47, 47, 47, 42, 42, 38, 38, 38, 38, 13, 13, 2, 5, 5, 38, 38, 38, 38] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429663173 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429663173 Building ZINC000337222470 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222470' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222470 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337222470 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222470/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222470 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/277 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@H](O)[C@@H]([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000337222470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337222470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000337222470 none C[C@@H]1CC[C@H](O)[C@@H]([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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.3', 'H', 'H', 'H', 'H', '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, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 49, 14, 49, 14, 14, 14, 14, 14, 8, 1, 8, 1, 1, 1, 4, 4, 1, 1, 4, 4, 49, 49, 49, 49, 49, 49, 49, 49, 147, 14, 14, 14, 14, 14, 14, 4, 4, 4, 4, 49, 49] 150 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 277 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222470 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222470/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222470 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/278 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/278' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@H](O)[C@@H]([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000337222470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337222470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000337222470 none C[C@@H]1CC[C@H](O)[C@@H]([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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.3', 'H', 'H', 'H', 'H', '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, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 14, 50, 14, 14, 14, 14, 14, 8, 1, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 150, 14, 14, 14, 14, 14, 14, 3, 3, 3, 3, 50, 50] 150 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 276 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222470 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337222470 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222470/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222470/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222470 Building ZINC000337222470 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222470' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222470 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337222470 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222470/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222470 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 277) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1CC[C@H](O)[C@@H]([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000337222470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337222470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000337222470 none C[C@@H]1CC[C@H](O)[C@@H]([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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.3', 'H', 'H', 'H', 'H', '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, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 49, 14, 49, 14, 14, 14, 14, 14, 8, 1, 8, 1, 1, 1, 4, 4, 1, 1, 4, 4, 49, 49, 49, 49, 49, 49, 49, 49, 147, 14, 14, 14, 14, 14, 14, 4, 4, 4, 4, 49, 49] 150 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 277 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222470 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222470/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222470 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 278) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1CC[C@H](O)[C@@H]([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000337222470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337222470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000337222470 none C[C@@H]1CC[C@H](O)[C@@H]([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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.3', 'H', 'H', 'H', 'H', '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, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 14, 50, 14, 14, 14, 14, 14, 8, 1, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 150, 14, 14, 14, 14, 14, 14, 3, 3, 3, 3, 50, 50] 150 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 276 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222470 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337222470 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222470/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222470/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222470 Building ZINC000337222471 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222471' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222471 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337222471 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222471/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222471 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/279 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@H](O)[C@@H]([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000337222471.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337222471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000337222471 none C[C@@H]1CC[C@H](O)[C@@H]([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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.3', 'H', 'H', 'H', 'H', '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, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 49, 13, 49, 13, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 4, 4, 1, 1, 4, 4, 49, 49, 49, 49, 49, 49, 49, 49, 147, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 49, 49] 150 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 273 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222471 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222471/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222471 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/280 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/280' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@H](O)[C@@H]([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000337222471.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337222471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000337222471 none C[C@@H]1CC[C@H](O)[C@@H]([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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.3', 'H', 'H', 'H', 'H', '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, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 47, 16, 47, 16, 16, 16, 16, 16, 9, 1, 9, 1, 1, 1, 4, 4, 1, 1, 4, 4, 47, 47, 47, 47, 47, 47, 47, 47, 141, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 47, 47] 150 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 263 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222471 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337222471 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222471/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222471/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222471 Building ZINC000337222471 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222471' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222471 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337222471 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222471/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222471 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 279) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/279: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@H](O)[C@@H]([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000337222471.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337222471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000337222471 none C[C@@H]1CC[C@H](O)[C@@H]([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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.3', 'H', 'H', 'H', 'H', '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, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 49, 13, 49, 13, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 4, 4, 1, 1, 4, 4, 49, 49, 49, 49, 49, 49, 49, 49, 147, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 49, 49] 150 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 273 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222471 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222471/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222471 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 280) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/280: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@H](O)[C@@H]([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000337222471.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337222471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000337222471 none C[C@@H]1CC[C@H](O)[C@@H]([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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.3', 'H', 'H', 'H', 'H', '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, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 47, 16, 47, 16, 16, 16, 16, 16, 9, 1, 9, 1, 1, 1, 4, 4, 1, 1, 4, 4, 47, 47, 47, 47, 47, 47, 47, 47, 141, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 47, 47] 150 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 263 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222471 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337222471 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222471/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222471/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222471 Building ZINC000337222472 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222472' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222472 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337222472 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222472/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222472 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/281 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@H](O)[C@H]([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000337222472.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337222472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000337222472 none C[C@@H]1CC[C@H](O)[C@H]([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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.3', 'H', 'H', 'H', 'H', '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, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 47, 20, 47, 20, 29, 20, 20, 20, 10, 1, 10, 1, 1, 1, 6, 6, 1, 6, 6, 6, 47, 47, 47, 47, 47, 47, 47, 47, 141, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 47, 47] 150 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 301 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222472 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222472/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222472 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/282 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/282' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@H](O)[C@H]([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000337222472.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337222472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222472/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000337222472 none C[C@@H]1CC[C@H](O)[C@H]([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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.3', 'H', 'H', 'H', 'H', '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, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 47, 21, 47, 21, 28, 21, 21, 21, 9, 1, 9, 1, 1, 1, 6, 6, 1, 1, 6, 6, 47, 47, 47, 47, 47, 47, 47, 47, 141, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 47, 47] 144 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 284 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222472 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337222472 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222472/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222472/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222472 Building ZINC000337222472 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222472' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222472 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337222472 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222472/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222472 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 281) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1CC[C@H](O)[C@H]([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000337222472.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337222472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000337222472 none C[C@@H]1CC[C@H](O)[C@H]([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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.3', 'H', 'H', 'H', 'H', '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, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 47, 20, 47, 20, 29, 20, 20, 20, 10, 1, 10, 1, 1, 1, 6, 6, 1, 6, 6, 6, 47, 47, 47, 47, 47, 47, 47, 47, 141, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 47, 47] 150 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 301 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222472 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222472/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222472 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 282) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1CC[C@H](O)[C@H]([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000337222472.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337222472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222472/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000337222472 none C[C@@H]1CC[C@H](O)[C@H]([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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.3', 'H', 'H', 'H', 'H', '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, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 47, 21, 47, 21, 28, 21, 21, 21, 9, 1, 9, 1, 1, 1, 6, 6, 1, 1, 6, 6, 47, 47, 47, 47, 47, 47, 47, 47, 141, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 47, 47] 144 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 284 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222472 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337222472 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222472/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222472/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222472 Building ZINC000337222473 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222473' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222473 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337222473 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222473/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222473 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/283 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@H](O)[C@H]([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000337222473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337222473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000337222473 none C[C@@H]1CC[C@H](O)[C@H]([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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.3', 'H', 'H', 'H', 'H', '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, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 35, 17, 35, 17, 22, 17, 17, 17, 9, 1, 9, 1, 1, 1, 5, 5, 1, 1, 5, 5, 35, 35, 35, 35, 35, 35, 35, 35, 105, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 35, 35] 111 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 212 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222473 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222473/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222473 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/284 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/284' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@H](O)[C@H]([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000337222473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337222473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000337222473 none C[C@@H]1CC[C@H](O)[C@H]([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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.3', 'H', 'H', 'H', 'H', '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, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 43, 17, 43, 17, 25, 17, 17, 17, 9, 1, 9, 1, 1, 1, 6, 6, 1, 1, 6, 6, 43, 43, 43, 43, 43, 43, 43, 43, 129, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 43, 43] 135 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 267 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222473 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337222473 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222473/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222473/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222473 Building ZINC000337222473 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222473' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222473 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337222473 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222473/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222473 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 283) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1CC[C@H](O)[C@H]([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000337222473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337222473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000337222473 none C[C@@H]1CC[C@H](O)[C@H]([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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.3', 'H', 'H', 'H', 'H', '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, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 35, 17, 35, 17, 22, 17, 17, 17, 9, 1, 9, 1, 1, 1, 5, 5, 1, 1, 5, 5, 35, 35, 35, 35, 35, 35, 35, 35, 105, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 35, 35] 111 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 212 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222473 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222473/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222473 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 284) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1CC[C@H](O)[C@H]([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000337222473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337222473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000337222473 none C[C@@H]1CC[C@H](O)[C@H]([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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.3', 'H', 'H', 'H', 'H', '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, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 43, 17, 43, 17, 25, 17, 17, 17, 9, 1, 9, 1, 1, 1, 6, 6, 1, 1, 6, 6, 43, 43, 43, 43, 43, 43, 43, 43, 129, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 43, 43] 135 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 267 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222473 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337222473 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222473/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222473/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337222473 Building ZINC000172071045 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071045' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071045 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172071045 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071045/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071045 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/285 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1cccs1) `ZINC000172071045.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172071045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000172071045 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 6, 6, 6, 4, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31] 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: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071045 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071045/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071045 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/286 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/286' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1cccs1) `ZINC000172071045.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172071045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000172071045 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 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] 0 hydrogens 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, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 28, 28, 28, 28, 7, 7, 7, 4, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28] 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: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071045 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000172071045 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071045/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071045/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071045 Building ZINC000172071045 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071045' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071045 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172071045 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071045/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071045 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 285) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1cccs1) `ZINC000172071045.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172071045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000172071045 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 6, 6, 6, 4, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31] 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: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071045 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071045/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071045 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 286) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1cccs1) `ZINC000172071045.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172071045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000172071045 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 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] 0 hydrogens 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, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 28, 28, 28, 28, 7, 7, 7, 4, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28] 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: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071045 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000172071045 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071045/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071045/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071045 Building ZINC000172071051 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071051' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071051 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172071051 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071051/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071051 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/287 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1cccs1) `ZINC000172071051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172071051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000172071051 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 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] 0 hydrogens 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, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 28, 28, 28, 28, 7, 7, 7, 4, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28] 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: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071051 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071051/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071051 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/288 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/288' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1cccs1) `ZINC000172071051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172071051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000172071051 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 6, 6, 6, 4, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31] 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: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071051 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000172071051 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071051/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071051/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071051 Building ZINC000172071051 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071051' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071051 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172071051 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071051/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071051 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 287) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1cccs1) `ZINC000172071051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172071051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000172071051 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 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] 0 hydrogens 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, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 28, 28, 28, 28, 7, 7, 7, 4, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28] 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: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071051 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071051/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071051 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 288) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1cccs1) `ZINC000172071051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172071051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000172071051 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 6, 6, 6, 4, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31] 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: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071051 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000172071051 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071051/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071051/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000172071051 Building ZINC000337227671 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337227671' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337227671 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337227671 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337227671/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337227671 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/289 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccncc1N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000337227671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337227671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337227671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000337227671 none Cc1ccncc1N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 8, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 29, 29, 29, 29, 13, 1, 18, 1, 1, 1, 4, 4, 1, 1, 4, 4, 29, 29, 48, 48, 48, 48, 48, 48, 29, 29, 29, 29, 4, 4, 4, 4, 29, 29, 29, 29] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 99 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337227671 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337227671/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337227671 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/290 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/290' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccncc1N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000337227671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337227671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337227671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000337227671 none Cc1ccncc1N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 8, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 29, 29, 29, 29, 12, 1, 17, 1, 1, 1, 4, 4, 1, 1, 4, 4, 29, 29, 49, 49, 49, 49, 49, 49, 29, 29, 29, 29, 4, 4, 4, 4, 29, 29, 29, 29] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 101 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337227671 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337227671 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337227671/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337227671/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337227671 Building ZINC000337227671 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337227671' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337227671 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337227671 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337227671/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337227671 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 289) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccncc1N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000337227671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337227671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337227671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000337227671 none Cc1ccncc1N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 8, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 29, 29, 29, 29, 13, 1, 18, 1, 1, 1, 4, 4, 1, 1, 4, 4, 29, 29, 48, 48, 48, 48, 48, 48, 29, 29, 29, 29, 4, 4, 4, 4, 29, 29, 29, 29] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 99 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337227671 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337227671/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337227671 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 290) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccncc1N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000337227671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337227671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337227671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000337227671 none Cc1ccncc1N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 8, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 29, 29, 29, 29, 12, 1, 17, 1, 1, 1, 4, 4, 1, 1, 4, 4, 29, 29, 49, 49, 49, 49, 49, 49, 29, 29, 29, 29, 4, 4, 4, 4, 29, 29, 29, 29] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 101 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337227671 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337227671 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337227671/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337227671/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337227671 Building ZINC000116705864 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000116705864' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000116705864 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000116705864 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000116705864/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000116705864 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/291 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@H]2COCCN2C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)o1) `ZINC000116705864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000116705864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000116705864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000116705864 none Cc1ccc([C@@H]2COCCN2C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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] 0 hydrogens 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, 14, 14, 14, 14, 14, 14, 12, 1, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 32, 32, 32, 32, 32, 32, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 62 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000116705864 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000116705864/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000116705864 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/292 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/292' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@H]2COCCN2C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)o1) `ZINC000116705864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000116705864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000116705864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000116705864 none Cc1ccc([C@@H]2COCCN2C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 12, 8, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000116705864 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000116705864 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000116705864/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000116705864/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000116705864 Building ZINC000116705864 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000116705864' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000116705864 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000116705864 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000116705864/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000116705864 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 291) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc([C@@H]2COCCN2C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)o1) `ZINC000116705864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000116705864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000116705864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000116705864 none Cc1ccc([C@@H]2COCCN2C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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] 0 hydrogens 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, 14, 14, 14, 14, 14, 14, 12, 1, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 32, 32, 32, 32, 32, 32, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 62 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000116705864 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000116705864/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000116705864 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 292) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc([C@@H]2COCCN2C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)o1) `ZINC000116705864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000116705864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000116705864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000116705864 none Cc1ccc([C@@H]2COCCN2C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 12, 8, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000116705864 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000116705864 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000116705864/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000116705864/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000116705864 Building ZINC000429784774 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429784774' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429784774 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429784774 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429784774/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429784774 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/293 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(CN2CCCC2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429784774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429784774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429784774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000429784774 none O=C(N1CCC(CN2CCCC2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 10, 10, 10, 10, 34, 34, 34, 34, 34, 10, 10, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 29, 29, 34, 34, 34, 34, 34, 34, 34, 34, 10, 10, 10, 10, 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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 111 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429784774 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429784774/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429784774 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/294 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/294' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(CN2CCCC2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429784774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429784774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429784774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000429784774 none O=C(N1CCC(CN2CCCC2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 7, 11, 11, 11, 11, 29, 29, 29, 29, 29, 11, 11, 1, 1, 1, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 27, 27, 29, 29, 29, 29, 29, 29, 29, 29, 11, 11, 11, 11, 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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429784774 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429784774 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429784774/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429784774/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429784774 Building ZINC000429784774 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429784774' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429784774 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429784774 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429784774/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429784774 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 293) grep: /scratch/xiaobo/83235/xao-8058115.15/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(N1CCC(CN2CCCC2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429784774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429784774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429784774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000429784774 none O=C(N1CCC(CN2CCCC2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 10, 10, 10, 10, 34, 34, 34, 34, 34, 10, 10, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 29, 29, 34, 34, 34, 34, 34, 34, 34, 34, 10, 10, 10, 10, 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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 111 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429784774 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429784774/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429784774 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 294) grep: /scratch/xiaobo/83235/xao-8058115.15/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(N1CCC(CN2CCCC2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429784774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429784774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429784774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000429784774 none O=C(N1CCC(CN2CCCC2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 7, 11, 11, 11, 11, 29, 29, 29, 29, 29, 11, 11, 1, 1, 1, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 27, 27, 29, 29, 29, 29, 29, 29, 29, 29, 11, 11, 11, 11, 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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429784774 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429784774 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429784774/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429784774/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429784774 Building ZINC000429795702 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429795702' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429795702 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429795702 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429795702/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429795702 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/295 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1c(F)cc(F)c(F)c1F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000429795702.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429795702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429795702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000429795702 none O=C(NCc1c(F)cc(F)c(F)c1F)[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', 'F', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 15, 1, 1, 15, 1, 15, 1, 15, 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, 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: [4, 1, 4, 4, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429795702 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429795702/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429795702 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/296 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/296' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1c(F)cc(F)c(F)c1F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000429795702.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429795702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429795702/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000429795702 none O=C(NCc1c(F)cc(F)c(F)c1F)[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', 'F', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 15, 1, 1, 15, 1, 15, 1, 15, 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, 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: [4, 1, 4, 4, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429795702 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429795702 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429795702/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429795702/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429795702 Building ZINC000429795702 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429795702' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429795702 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429795702 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429795702/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429795702 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 295) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NCc1c(F)cc(F)c(F)c1F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000429795702.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429795702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429795702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000429795702 none O=C(NCc1c(F)cc(F)c(F)c1F)[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', 'F', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 15, 1, 1, 15, 1, 15, 1, 15, 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, 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: [4, 1, 4, 4, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429795702 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429795702/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429795702 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 296) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NCc1c(F)cc(F)c(F)c1F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000429795702.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429795702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429795702/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000429795702 none O=C(NCc1c(F)cc(F)c(F)c1F)[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', 'F', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 15, 1, 1, 15, 1, 15, 1, 15, 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, 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: [4, 1, 4, 4, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429795702 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429795702 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429795702/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429795702/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429795702 Building ZINC000788547106 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547106' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547106 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000788547106 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547106/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547106 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/297 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H](O)c1ccccc1) `ZINC000788547106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000788547106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000788547106 none CC(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 14, 31, 5, 14, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 14, 33, 33, 33, 39, 39, 33, 39, 39, 31, 31, 31, 31, 31, 31, 31, 5, 5, 5, 5, 5, 99, 39, 39, 33, 39, 39] 150 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 334 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547106 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547106/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547106 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/298 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/298' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H](O)c1ccccc1) `ZINC000788547106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000788547106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000788547106 none CC(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [33, 16, 31, 5, 16, 5, 1, 5, 1, 1, 1, 5, 5, 1, 2, 5, 5, 16, 40, 40, 40, 48, 48, 45, 48, 48, 33, 33, 33, 33, 33, 33, 33, 5, 5, 5, 5, 5, 120, 48, 48, 40, 48, 48] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 406 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547106 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000788547106 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547106/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547106/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547106 Building ZINC000788547106 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547106' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547106 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000788547106 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547106/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547106 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 297) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/297: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H](O)c1ccccc1) `ZINC000788547106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000788547106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000788547106 none CC(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 14, 31, 5, 14, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 14, 33, 33, 33, 39, 39, 33, 39, 39, 31, 31, 31, 31, 31, 31, 31, 5, 5, 5, 5, 5, 99, 39, 39, 33, 39, 39] 150 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 334 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547106 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547106/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547106 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 298) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/298: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H](O)c1ccccc1) `ZINC000788547106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000788547106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000788547106 none CC(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [33, 16, 31, 5, 16, 5, 1, 5, 1, 1, 1, 5, 5, 1, 2, 5, 5, 16, 40, 40, 40, 48, 48, 45, 48, 48, 33, 33, 33, 33, 33, 33, 33, 5, 5, 5, 5, 5, 120, 48, 48, 40, 48, 48] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 406 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547106 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000788547106 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547106/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547106/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547106 Building ZINC000788547109 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547109' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547109 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000788547109 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547109/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547109 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/299 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H](O)c1ccccc1) `ZINC000788547109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000788547109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000788547109 none CC(C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 13, 32, 6, 13, 6, 1, 6, 1, 1, 1, 4, 4, 2, 2, 4, 4, 13, 36, 36, 36, 40, 40, 36, 40, 40, 32, 32, 32, 32, 32, 32, 32, 6, 4, 4, 4, 4, 108, 40, 40, 36, 40, 40] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 365 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547109 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547109/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547109 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/300 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/300' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H](O)c1ccccc1) `ZINC000788547109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000788547109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000788547109 none CC(C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 14, 30, 6, 14, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 36, 36, 36, 40, 40, 40, 40, 40, 30, 30, 30, 30, 30, 30, 30, 6, 3, 3, 3, 3, 108, 40, 40, 40, 40, 40] 150 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 340 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547109 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000788547109 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547109/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547109/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547109 Building ZINC000788547109 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547109' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547109 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000788547109 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547109/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547109 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 299) grep: /scratch/xiaobo/83235/xao-8058115.15/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)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H](O)c1ccccc1) `ZINC000788547109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000788547109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000788547109 none CC(C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 13, 32, 6, 13, 6, 1, 6, 1, 1, 1, 4, 4, 2, 2, 4, 4, 13, 36, 36, 36, 40, 40, 36, 40, 40, 32, 32, 32, 32, 32, 32, 32, 6, 4, 4, 4, 4, 108, 40, 40, 36, 40, 40] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 365 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547109 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547109/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547109 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 300) grep: /scratch/xiaobo/83235/xao-8058115.15/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)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H](O)c1ccccc1) `ZINC000788547109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000788547109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000788547109 none CC(C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 14, 30, 6, 14, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 36, 36, 36, 40, 40, 40, 40, 40, 30, 30, 30, 30, 30, 30, 30, 6, 3, 3, 3, 3, 108, 40, 40, 40, 40, 40] 150 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 340 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547109 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000788547109 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547109/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547109/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547109 Building ZINC000788547116 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547116' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547116 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000788547116 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547116/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547116 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/301 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@@H](O)c1ccccc1) `ZINC000788547116.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000788547116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000788547116 none CC(C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 17, 35, 6, 17, 6, 1, 6, 1, 1, 1, 5, 5, 2, 4, 5, 5, 17, 38, 38, 38, 42, 42, 38, 42, 42, 35, 35, 35, 35, 35, 35, 35, 6, 5, 5, 5, 5, 114, 42, 42, 38, 42, 42] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 381 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547116 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547116/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547116 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/302 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/302' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@@H](O)c1ccccc1) `ZINC000788547116.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000788547116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000788547116 none CC(C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 15, 32, 4, 15, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 15, 44, 44, 44, 48, 48, 44, 48, 48, 32, 32, 32, 32, 32, 32, 32, 4, 5, 5, 5, 5, 132, 48, 48, 44, 48, 48] 150 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 425 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547116 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000788547116 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547116/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547116/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547116 Building ZINC000788547116 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547116' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547116 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000788547116 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547116/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547116 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 301) grep: /scratch/xiaobo/83235/xao-8058115.15/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)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@@H](O)c1ccccc1) `ZINC000788547116.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000788547116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000788547116 none CC(C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 17, 35, 6, 17, 6, 1, 6, 1, 1, 1, 5, 5, 2, 4, 5, 5, 17, 38, 38, 38, 42, 42, 38, 42, 42, 35, 35, 35, 35, 35, 35, 35, 6, 5, 5, 5, 5, 114, 42, 42, 38, 42, 42] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 381 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547116 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547116/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547116 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 302) grep: /scratch/xiaobo/83235/xao-8058115.15/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)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@@H](O)c1ccccc1) `ZINC000788547116.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000788547116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000788547116 none CC(C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 15, 32, 4, 15, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 15, 44, 44, 44, 48, 48, 44, 48, 48, 32, 32, 32, 32, 32, 32, 32, 4, 5, 5, 5, 5, 132, 48, 48, 44, 48, 48] 150 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 425 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547116 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000788547116 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547116/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547116/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788547116 Building ZINC000130760838 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130760838' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130760838 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000130760838 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130760838/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130760838 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/303 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCO[C@@]2(CCSC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000130760838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000130760838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130760838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000130760838 none O=C(N[C@@H]1CCO[C@@]2(CCSC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130760838 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130760838/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130760838 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/304 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/304' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCO[C@@]2(CCSC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000130760838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000130760838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130760838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000130760838 none O=C(N[C@@H]1CCO[C@@]2(CCSC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 21, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130760838 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000130760838 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130760838/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130760838/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130760838 Building ZINC000130760838 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130760838' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130760838 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000130760838 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130760838/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130760838 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 303) grep: /scratch/xiaobo/83235/xao-8058115.15/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(N[C@@H]1CCO[C@@]2(CCSC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000130760838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000130760838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130760838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000130760838 none O=C(N[C@@H]1CCO[C@@]2(CCSC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130760838 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130760838/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130760838 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 304) grep: /scratch/xiaobo/83235/xao-8058115.15/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(N[C@@H]1CCO[C@@]2(CCSC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000130760838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000130760838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130760838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000130760838 none O=C(N[C@@H]1CCO[C@@]2(CCSC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 21, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130760838 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000130760838 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130760838/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130760838/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130760838 Building ZINC000130761090 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130761090' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130761090 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000130761090 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130761090/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130761090 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/305 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCO[C@@]2(CCSC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000130761090.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000130761090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130761090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000130761090 none O=C(N[C@H]1CCO[C@@]2(CCSC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 23, 23, 23, 23, 23, 23, 23, 23, 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, 45, 46]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130761090 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130761090/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130761090 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/306 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/306' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCO[C@@]2(CCSC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000130761090.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000130761090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130761090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000130761090 none O=C(N[C@H]1CCO[C@@]2(CCSC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130761090 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000130761090 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130761090/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130761090/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130761090 Building ZINC000130761090 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130761090' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130761090 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000130761090 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130761090/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130761090 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 305) grep: /scratch/xiaobo/83235/xao-8058115.15/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(N[C@H]1CCO[C@@]2(CCSC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000130761090.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000130761090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130761090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000130761090 none O=C(N[C@H]1CCO[C@@]2(CCSC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 23, 23, 23, 23, 23, 23, 23, 23, 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, 45, 46]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130761090 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130761090/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130761090 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 306) grep: /scratch/xiaobo/83235/xao-8058115.15/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(N[C@H]1CCO[C@@]2(CCSC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000130761090.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000130761090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130761090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000130761090 none O=C(N[C@H]1CCO[C@@]2(CCSC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130761090 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000130761090 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130761090/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130761090/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000130761090 Building ZINC001126737288 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001126737288' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001126737288 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001126737288 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001126737288/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001126737288 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/307 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(=O)n(C)cc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001126737288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001126737288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001126737288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001126737288 none Cc1cc(=O)n(C)cc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 34, 9, 9, 1, 9, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 9, 6, 1, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 65 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001126737288 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001126737288/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001126737288 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/308 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/308' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(=O)n(C)cc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001126737288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001126737288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001126737288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001126737288 none Cc1cc(=O)n(C)cc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 34, 9, 9, 1, 9, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 9, 6, 1, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 65 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001126737288 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC001126737288 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001126737288/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001126737288/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001126737288 Building ZINC001126737288 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001126737288' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001126737288 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001126737288 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001126737288/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001126737288 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 307) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1cc(=O)n(C)cc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001126737288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001126737288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001126737288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001126737288 none Cc1cc(=O)n(C)cc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 34, 9, 9, 1, 9, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 9, 6, 1, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 65 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001126737288 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001126737288/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001126737288 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 308) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1cc(=O)n(C)cc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001126737288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001126737288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001126737288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001126737288 none Cc1cc(=O)n(C)cc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 34, 9, 9, 1, 9, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 9, 6, 1, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 65 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001126737288 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC001126737288 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001126737288/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001126737288/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001126737288 Building ZINC000753858166 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000753858166' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000753858166 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000753858166 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000753858166/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000753858166 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/309 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)OCc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000753858166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000753858166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000753858166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000753858166 none C[C@@H](CC(=O)OCc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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, 5, 7, 5, 1, 11, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 13, 33, 33, 33, 49, 50, 50, 49, 50, 50, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 5, 5, 13, 13, 49, 49, 50, 50, 50, 50, 50, 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000753858166 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000753858166/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000753858166 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/310 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/310' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)OCc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000753858166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000753858166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000753858166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000753858166 none C[C@@H](CC(=O)OCc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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, 5, 7, 5, 1, 11, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 10, 33, 33, 33, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 4, 4, 10, 10, 50, 50, 50, 50, 50, 50, 50, 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]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000753858166 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000753858166 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000753858166/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000753858166/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000753858166 Building ZINC000753858166 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000753858166' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000753858166 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000753858166 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000753858166/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000753858166 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 309) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/309: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)OCc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000753858166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000753858166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000753858166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000753858166 none C[C@@H](CC(=O)OCc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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, 5, 7, 5, 1, 11, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 13, 33, 33, 33, 49, 50, 50, 49, 50, 50, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 5, 5, 13, 13, 49, 49, 50, 50, 50, 50, 50, 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000753858166 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000753858166/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000753858166 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 310) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/310: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)OCc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000753858166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000753858166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000753858166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000753858166 none C[C@@H](CC(=O)OCc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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, 5, 7, 5, 1, 11, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 10, 33, 33, 33, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 4, 4, 10, 10, 50, 50, 50, 50, 50, 50, 50, 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]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000753858166 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000753858166 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000753858166/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000753858166/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000753858166 Building ZINC000429889241 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000429889241 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/311 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429889241.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429889241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429889241 none CC[N@]1CC[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 44, 44, 44, 30, 44, 14, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 44, 44, 49, 49, 49, 49, 49, 44, 44, 44, 44, 25, 25, 14, 14, 2, 4, 4, 44, 44, 44, 44] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 200 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/312 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/312' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429889241.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429889241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429889241 none CC[N@]1CC[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 44, 44, 44, 30, 44, 14, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 44, 44, 49, 49, 49, 49, 49, 44, 44, 44, 44, 25, 25, 14, 14, 2, 4, 4, 44, 44, 44, 44] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 200 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/313 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/313' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[C@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429889241.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000429889241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429889241 none CC[N@]1CC[C@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 46, 46, 46, 28, 46, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 46, 46, 49, 49, 49, 49, 49, 46, 46, 46, 46, 23, 23, 13, 13, 2, 4, 4, 46, 46, 46, 46] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 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: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/314 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/314' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429889241.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000429889241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429889241 none CC[N@]1CC[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 46, 46, 46, 28, 46, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 46, 46, 49, 49, 49, 49, 49, 46, 46, 46, 46, 23, 23, 13, 13, 2, 4, 4, 46, 46, 46, 46] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 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: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429889241 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 Building ZINC000429889241 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000429889241 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 311) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC[N@]1CC[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429889241.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429889241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429889241 none CC[N@]1CC[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 44, 44, 44, 30, 44, 14, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 44, 44, 49, 49, 49, 49, 49, 44, 44, 44, 44, 25, 25, 14, 14, 2, 4, 4, 44, 44, 44, 44] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 200 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 312) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC[N@]1CC[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429889241.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429889241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429889241 none CC[N@]1CC[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 44, 44, 44, 30, 44, 14, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 44, 44, 49, 49, 49, 49, 49, 44, 44, 44, 44, 25, 25, 14, 14, 2, 4, 4, 44, 44, 44, 44] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 200 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 313) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC[N@]1CC[C@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429889241.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000429889241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429889241 none CC[N@]1CC[C@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 46, 46, 46, 28, 46, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 46, 46, 49, 49, 49, 49, 49, 46, 46, 46, 46, 23, 23, 13, 13, 2, 4, 4, 46, 46, 46, 46] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 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: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 314) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC[N@]1CC[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429889241.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000429889241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429889241 none CC[N@]1CC[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 46, 46, 46, 28, 46, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 46, 46, 49, 49, 49, 49, 49, 46, 46, 46, 46, 23, 23, 13, 13, 2, 4, 4, 46, 46, 46, 46] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 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: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429889241 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 Building ZINC000429889241 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000429889241 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 311) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC[N@]1CC[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429889241.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429889241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429889241 none CC[N@]1CC[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 44, 44, 44, 30, 44, 14, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 44, 44, 49, 49, 49, 49, 49, 44, 44, 44, 44, 25, 25, 14, 14, 2, 4, 4, 44, 44, 44, 44] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 200 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 312) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC[N@]1CC[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429889241.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429889241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429889241 none CC[N@]1CC[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 44, 44, 44, 30, 44, 14, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 44, 44, 49, 49, 49, 49, 49, 44, 44, 44, 44, 25, 25, 14, 14, 2, 4, 4, 44, 44, 44, 44] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 200 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 313) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC[N@]1CC[C@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429889241.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000429889241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429889241 none CC[N@]1CC[C@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 46, 46, 46, 28, 46, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 46, 46, 49, 49, 49, 49, 49, 46, 46, 46, 46, 23, 23, 13, 13, 2, 4, 4, 46, 46, 46, 46] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 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: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 314) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC[N@]1CC[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429889241.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000429889241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429889241 none CC[N@]1CC[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 46, 46, 46, 28, 46, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 46, 46, 49, 49, 49, 49, 49, 46, 46, 46, 46, 23, 23, 13, 13, 2, 4, 4, 46, 46, 46, 46] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 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: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429889241 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 Building ZINC000429889241 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000429889241 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 311) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC[N@]1CC[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429889241.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429889241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429889241 none CC[N@]1CC[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 44, 44, 44, 30, 44, 14, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 44, 44, 49, 49, 49, 49, 49, 44, 44, 44, 44, 25, 25, 14, 14, 2, 4, 4, 44, 44, 44, 44] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 200 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 312) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC[N@]1CC[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429889241.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429889241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429889241 none CC[N@]1CC[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 44, 44, 44, 30, 44, 14, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 44, 44, 49, 49, 49, 49, 49, 44, 44, 44, 44, 25, 25, 14, 14, 2, 4, 4, 44, 44, 44, 44] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 200 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 313) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC[N@]1CC[C@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429889241.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000429889241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429889241 none CC[N@]1CC[C@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 46, 46, 46, 28, 46, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 46, 46, 49, 49, 49, 49, 49, 46, 46, 46, 46, 23, 23, 13, 13, 2, 4, 4, 46, 46, 46, 46] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 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: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 314) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC[N@]1CC[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429889241.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000429889241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000429889241 none CC[N@]1CC[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 46, 46, 46, 28, 46, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 46, 46, 49, 49, 49, 49, 49, 46, 46, 46, 46, 23, 23, 13, 13, 2, 4, 4, 46, 46, 46, 46] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 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: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429889241 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429889241 Building ZINC000862637262 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862637262' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862637262 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000862637262 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862637262/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862637262 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/315 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1Cc2ccccc2O[C@H]1C(F)(F)F) `ZINC000862637262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000862637262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862637262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000862637262 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1Cc2ccccc2O[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 7, 7, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 20, 20, 20, 20, 20, 20] 20 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 57 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862637262 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862637262/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862637262 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/316 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/316' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1Cc2ccccc2O[C@H]1C(F)(F)F) `ZINC000862637262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000862637262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862637262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000862637262 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1Cc2ccccc2O[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 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, 1, 3, 3, 1, 1, 1, 6, 6, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 17, 17, 17, 17, 17, 17] 18 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862637262 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000862637262 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862637262/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862637262/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862637262 Building ZINC000862637262 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862637262' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862637262 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000862637262 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862637262/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862637262 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 315) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1Cc2ccccc2O[C@H]1C(F)(F)F) `ZINC000862637262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000862637262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862637262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000862637262 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1Cc2ccccc2O[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 7, 7, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 20, 20, 20, 20, 20, 20] 20 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 57 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862637262 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862637262/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862637262 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 316) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1Cc2ccccc2O[C@H]1C(F)(F)F) `ZINC000862637262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000862637262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862637262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000862637262 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1Cc2ccccc2O[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 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, 1, 3, 3, 1, 1, 1, 6, 6, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 17, 17, 17, 17, 17, 17] 18 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862637262 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000862637262 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862637262/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862637262/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862637262 Building ZINC000429898015 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429898015' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429898015 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429898015 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429898015/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429898015 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/317 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Cn1ccnc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429898015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429898015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429898015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000429898015 none CC(C)Cn1ccnc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 23, 23, 23, 23, 23, 14, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 23, 23, 14, 14, 4, 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429898015 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429898015/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429898015 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/318 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/318' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Cn1ccnc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429898015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429898015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429898015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000429898015 none CC(C)Cn1ccnc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 22, 22, 22, 22, 22, 15, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 35, 35, 35, 35, 35, 35, 35, 35, 35, 22, 22, 15, 15, 4, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429898015 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429898015 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429898015/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429898015/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429898015 Building ZINC000429898015 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429898015' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429898015 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429898015 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429898015/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429898015 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 317) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)Cn1ccnc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429898015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429898015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429898015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000429898015 none CC(C)Cn1ccnc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 23, 23, 23, 23, 23, 14, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 23, 23, 14, 14, 4, 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429898015 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429898015/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429898015 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 318) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)Cn1ccnc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429898015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429898015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429898015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000429898015 none CC(C)Cn1ccnc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 22, 22, 22, 22, 22, 15, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 35, 35, 35, 35, 35, 35, 35, 35, 35, 22, 22, 15, 15, 4, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429898015 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429898015 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429898015/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429898015/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429898015 Building ZINC000726149442 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000726149442' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000726149442 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000726149442 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000726149442/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000726149442 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/319 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C(F)(F)F)n2)cn1) `ZINC000726149442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000726149442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000726149442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000726149442 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C(F)(F)F)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 12, 19, 19, 12, 12, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 12, 6, 11, 11, 11, 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000726149442 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000726149442/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000726149442 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/320 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/320' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C(F)(F)F)n2)cn1) `ZINC000726149442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000726149442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000726149442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000726149442 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C(F)(F)F)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 12, 12, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 27, 27, 27, 27, 27, 27, 27, 27, 27, 12, 6, 11, 11, 11, 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000726149442 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000726149442 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000726149442/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000726149442/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000726149442 Building ZINC000726149442 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000726149442' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000726149442 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000726149442 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000726149442/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000726149442 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 319) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C(F)(F)F)n2)cn1) `ZINC000726149442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000726149442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000726149442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000726149442 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C(F)(F)F)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 12, 19, 19, 12, 12, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 12, 6, 11, 11, 11, 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000726149442 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000726149442/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000726149442 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 320) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C(F)(F)F)n2)cn1) `ZINC000726149442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000726149442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000726149442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000726149442 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C(F)(F)F)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 12, 12, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 27, 27, 27, 27, 27, 27, 27, 27, 27, 12, 6, 11, 11, 11, 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000726149442 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000726149442 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000726149442/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000726149442/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000726149442 Building ZINC000429987711 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987711' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987711 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429987711 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987711/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987711 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/321 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCC[C@@H](C)N1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429987711.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429987711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000429987711 none C[C@@H]1CCC[C@@H](C)N1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 39, 39, 39, 39, 38, 19, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 27, 27, 19, 19, 4, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 129 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987711 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987711/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987711 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/322 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/322' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCC[C@@H](C)N1CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429987711.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429987711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987711/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000429987711 none C[C@@H]1CCC[C@@H](C)N1CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 21, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 27, 27, 21, 21, 4, 7, 7] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 130 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987711 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429987711 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987711/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987711/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987711 Building ZINC000429987711 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987711' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987711 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429987711 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987711/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987711 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 321) grep: /scratch/xiaobo/83235/xao-8058115.15/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]1CCC[C@@H](C)N1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429987711.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429987711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000429987711 none C[C@@H]1CCC[C@@H](C)N1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 39, 39, 39, 39, 38, 19, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 27, 27, 19, 19, 4, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 129 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987711 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987711/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987711 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 322) grep: /scratch/xiaobo/83235/xao-8058115.15/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]1CCC[C@@H](C)N1CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429987711.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429987711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987711/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000429987711 none C[C@@H]1CCC[C@@H](C)N1CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 21, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 27, 27, 21, 21, 4, 7, 7] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 130 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987711 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429987711 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987711/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987711/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987711 Building ZINC000429987713 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987713' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987713 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429987713 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987713/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987713 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/323 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCC[C@H](C)N1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429987713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429987713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000429987713 none C[C@@H]1CCC[C@H](C)N1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 29, 29, 29, 29, 29, 6, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 11, 11] 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987713 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987713/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987713 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/324 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/324' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCC[C@H](C)N1CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429987713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429987713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000429987713 none C[C@@H]1CCC[C@H](C)N1CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 29, 29, 29, 29, 29, 6, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 11, 11] 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987713 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429987713 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987713/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987713/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987713 Building ZINC000429987713 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987713' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987713 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429987713 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987713/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987713 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 323) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1CCC[C@H](C)N1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429987713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429987713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000429987713 none C[C@@H]1CCC[C@H](C)N1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 29, 29, 29, 29, 29, 6, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 11, 11] 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987713 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987713/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987713 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 324) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1CCC[C@H](C)N1CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429987713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429987713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000429987713 none C[C@@H]1CCC[C@H](C)N1CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 29, 29, 29, 29, 29, 6, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 11, 11] 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987713 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429987713 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987713/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987713/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987713 Building ZINC000429987716 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987716' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987716 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429987716 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987716/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987716 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/325 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCC[C@H](C)N1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429987716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429987716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000429987716 none C[C@H]1CCC[C@H](C)N1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 36, 36, 35, 20, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 26, 26, 20, 20, 4, 7, 7] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 126 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987716 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987716/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987716 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/326 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/326' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCC[C@H](C)N1CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429987716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429987716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000429987716 none C[C@H]1CCC[C@H](C)N1CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 39, 39, 39, 39, 38, 19, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 27, 27, 19, 19, 4, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 129 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987716 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429987716 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987716/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987716/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987716 Building ZINC000429987716 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987716' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987716 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429987716 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987716/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987716 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 325) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H]1CCC[C@H](C)N1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429987716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429987716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000429987716 none C[C@H]1CCC[C@H](C)N1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 36, 36, 35, 20, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 26, 26, 20, 20, 4, 7, 7] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 126 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987716 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987716/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987716 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 326) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H]1CCC[C@H](C)N1CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429987716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429987716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000429987716 none C[C@H]1CCC[C@H](C)N1CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 39, 39, 39, 39, 38, 19, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 27, 27, 19, 19, 4, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 129 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987716 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000429987716 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987716/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987716/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000429987716 Building ZINC000754025608 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754025608' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754025608 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000754025608 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754025608/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754025608 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/327 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754025608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754025608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754025608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000754025608 none O=C(NC1CC1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 29, 29, 47, 47, 18, 18, 18, 18, 18, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 33, 47, 47, 47, 47, 47, 18, 18, 18, 18, 6, 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, 38]) total number of confs: 152 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754025608 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754025608/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754025608 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/328 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/328' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754025608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754025608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754025608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000754025608 none O=C(NC1CC1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 29, 29, 47, 47, 18, 18, 18, 18, 18, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 33, 47, 47, 47, 47, 47, 18, 18, 18, 18, 6, 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, 38]) total number of confs: 152 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754025608 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000754025608 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754025608/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754025608/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754025608 Building ZINC000754025608 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754025608' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754025608 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000754025608 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754025608/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754025608 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 327) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/327: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754025608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754025608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754025608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000754025608 none O=C(NC1CC1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 29, 29, 47, 47, 18, 18, 18, 18, 18, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 33, 47, 47, 47, 47, 47, 18, 18, 18, 18, 6, 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, 38]) total number of confs: 152 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754025608 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754025608/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754025608 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 328) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/328: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754025608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754025608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754025608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000754025608 none O=C(NC1CC1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 29, 29, 47, 47, 18, 18, 18, 18, 18, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 33, 47, 47, 47, 47, 47, 18, 18, 18, 18, 6, 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, 38]) total number of confs: 152 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754025608 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000754025608 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754025608/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754025608/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754025608 Building ZINC000927579118 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579118' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579118 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927579118 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579118/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579118 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/329 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CC[C@@H](C(F)(F)F)O1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000927579118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927579118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000927579118 none O=C(NC[C@@H]1CC[C@@H](C(F)(F)F)O1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 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] 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: [3, 1, 3, 3, 22, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 3, 18, 18, 30, 30, 30, 30, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579118 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579118/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579118 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/330 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/330' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CC[C@@H](C(F)(F)F)O1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000927579118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927579118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000927579118 none O=C(NC[C@@H]1CC[C@@H](C(F)(F)F)O1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 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] 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: [3, 1, 3, 3, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 3, 15, 15, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/83235/xao-8058115.15/working/building/ZINC000927579118 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000927579118 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579118/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579118/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579118 Building ZINC000927579118 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579118' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579118 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927579118 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579118/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579118 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 329) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@@H]1CC[C@@H](C(F)(F)F)O1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000927579118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927579118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000927579118 none O=C(NC[C@@H]1CC[C@@H](C(F)(F)F)O1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 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] 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: [3, 1, 3, 3, 22, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 3, 18, 18, 30, 30, 30, 30, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579118 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579118/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579118 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 330) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@@H]1CC[C@@H](C(F)(F)F)O1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000927579118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927579118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000927579118 none O=C(NC[C@@H]1CC[C@@H](C(F)(F)F)O1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 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] 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: [3, 1, 3, 3, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 3, 15, 15, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/83235/xao-8058115.15/working/building/ZINC000927579118 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000927579118 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579118/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579118/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579118 Building ZINC000927579121 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579121' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579121 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927579121 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579121/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579121 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/331 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[C@@H](C(F)(F)F)O1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000927579121.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927579121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000927579121 none O=C(NC[C@H]1CC[C@@H](C(F)(F)F)O1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 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] 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: [2, 1, 2, 2, 19, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 13, 13, 30, 30, 30, 30, 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: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579121 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579121/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579121 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/332 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/332' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[C@@H](C(F)(F)F)O1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000927579121.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927579121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579121/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000927579121 none O=C(NC[C@H]1CC[C@@H](C(F)(F)F)O1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 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] 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: [3, 1, 3, 3, 24, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 16, 16, 35, 35, 35, 35, 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: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579121 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000927579121 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579121/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579121/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579121 Building ZINC000927579121 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579121' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579121 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927579121 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579121/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579121 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 331) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@H]1CC[C@@H](C(F)(F)F)O1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000927579121.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927579121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000927579121 none O=C(NC[C@H]1CC[C@@H](C(F)(F)F)O1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 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] 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: [2, 1, 2, 2, 19, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 13, 13, 30, 30, 30, 30, 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: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579121 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579121/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579121 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 332) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@H]1CC[C@@H](C(F)(F)F)O1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000927579121.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927579121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579121/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000927579121 none O=C(NC[C@H]1CC[C@@H](C(F)(F)F)O1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 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] 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: [3, 1, 3, 3, 24, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 16, 16, 35, 35, 35, 35, 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: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579121 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000927579121 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579121/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579121/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579121 Building ZINC000927579124 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579124' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579124 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927579124 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579124/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579124 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/333 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CC[C@H](C(F)(F)F)O1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000927579124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927579124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000927579124 none O=C(NC[C@@H]1CC[C@H](C(F)(F)F)O1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 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] 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: [3, 1, 3, 3, 25, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 16, 16, 36, 36, 36, 36, 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: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579124 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579124/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579124 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/334 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/334' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CC[C@H](C(F)(F)F)O1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000927579124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927579124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000927579124 none O=C(NC[C@@H]1CC[C@H](C(F)(F)F)O1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 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] 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: [2, 1, 2, 2, 21, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 14, 14, 30, 30, 30, 30, 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: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579124 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000927579124 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579124/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579124/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579124 Building ZINC000927579124 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579124' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579124 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927579124 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579124/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579124 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 333) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@@H]1CC[C@H](C(F)(F)F)O1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000927579124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927579124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000927579124 none O=C(NC[C@@H]1CC[C@H](C(F)(F)F)O1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 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] 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: [3, 1, 3, 3, 25, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 16, 16, 36, 36, 36, 36, 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: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579124 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579124/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579124 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 334) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@@H]1CC[C@H](C(F)(F)F)O1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000927579124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927579124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000927579124 none O=C(NC[C@@H]1CC[C@H](C(F)(F)F)O1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 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] 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: [2, 1, 2, 2, 21, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 14, 14, 30, 30, 30, 30, 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: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579124 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000927579124 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579124/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579124/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579124 Building ZINC000927579126 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579126' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579126 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927579126 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579126/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579126 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/335 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[C@H](C(F)(F)F)O1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000927579126.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927579126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000927579126 none O=C(NC[C@H]1CC[C@H](C(F)(F)F)O1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 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] 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: [3, 1, 3, 3, 17, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 3, 15, 15, 30, 30, 30, 30, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579126 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579126/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579126 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/336 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/336' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[C@H](C(F)(F)F)O1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000927579126.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927579126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000927579126 none O=C(NC[C@H]1CC[C@H](C(F)(F)F)O1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 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] 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: [3, 1, 3, 3, 21, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 17, 17, 30, 30, 30, 30, 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: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579126 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000927579126 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579126/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579126/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579126 Building ZINC000927579126 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579126' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579126 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927579126 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579126/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579126 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 335) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@H]1CC[C@H](C(F)(F)F)O1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000927579126.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927579126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000927579126 none O=C(NC[C@H]1CC[C@H](C(F)(F)F)O1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 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] 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: [3, 1, 3, 3, 17, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 3, 15, 15, 30, 30, 30, 30, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579126 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579126/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579126 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 336) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@H]1CC[C@H](C(F)(F)F)O1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000927579126.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927579126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000927579126 none O=C(NC[C@H]1CC[C@H](C(F)(F)F)O1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 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] 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: [3, 1, 3, 3, 21, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 17, 17, 30, 30, 30, 30, 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: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579126 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000927579126 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579126/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579126/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927579126 Building ZINC000754109774 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754109774' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754109774 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000754109774 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754109774/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754109774 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/337 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754109774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754109774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754109774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000754109774 none CC(C)NC(=O)c1ccccc1NC(=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', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 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, 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, 4, 9, 6, 8, 10, 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: [46, 35, 46, 35, 14, 39, 14, 14, 13, 14, 14, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 2, 4, 4, 46, 46, 46, 46, 46, 46, 46, 39, 14, 14, 14, 14, 6, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 170 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754109774 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754109774/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754109774 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/338 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/338' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754109774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754109774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754109774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000754109774 none CC(C)NC(=O)c1ccccc1NC(=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', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 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, 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, 4, 9, 6, 8, 10, 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: [46, 35, 46, 35, 15, 39, 15, 15, 15, 15, 15, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 2, 5, 5, 46, 46, 46, 46, 46, 46, 46, 39, 15, 15, 15, 15, 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: 166 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754109774 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000754109774 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754109774/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754109774/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754109774 Building ZINC000754109774 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754109774' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754109774 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000754109774 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754109774/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754109774 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 337) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)NC(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754109774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754109774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754109774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000754109774 none CC(C)NC(=O)c1ccccc1NC(=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', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 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, 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, 4, 9, 6, 8, 10, 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: [46, 35, 46, 35, 14, 39, 14, 14, 13, 14, 14, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 2, 4, 4, 46, 46, 46, 46, 46, 46, 46, 39, 14, 14, 14, 14, 6, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 170 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754109774 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754109774/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754109774 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 338) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)NC(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754109774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754109774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754109774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000754109774 none CC(C)NC(=O)c1ccccc1NC(=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', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 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, 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, 4, 9, 6, 8, 10, 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: [46, 35, 46, 35, 15, 39, 15, 15, 15, 15, 15, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 2, 5, 5, 46, 46, 46, 46, 46, 46, 46, 39, 15, 15, 15, 15, 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: 166 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754109774 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000754109774 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754109774/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754109774/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754109774 Building ZINC000754535841 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754535841' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754535841 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000754535841 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754535841/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754535841 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/339 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc(C2CCN(C(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)CC2)n1) `ZINC000754535841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754535841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754535841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000754535841 none Cc1ccnc(C2CCN(C(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 1, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 12, 12, 50, 50, 50, 50, 12, 50, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 12, 12, 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754535841 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754535841/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754535841 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/340 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/340' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)CC2)n1) `ZINC000754535841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754535841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754535841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000754535841 none Cc1ccnc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 11, 50, 50, 11, 11, 11, 11, 7, 1, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 11, 11, 50, 50, 50, 50, 11, 50, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 11, 11, 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754535841 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000754535841 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754535841/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754535841/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754535841 Building ZINC000754535841 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754535841' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754535841 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000754535841 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754535841/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754535841 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 339) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccnc(C2CCN(C(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)CC2)n1) `ZINC000754535841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754535841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754535841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000754535841 none Cc1ccnc(C2CCN(C(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 1, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 12, 12, 50, 50, 50, 50, 12, 50, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 12, 12, 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754535841 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754535841/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754535841 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 340) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccnc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)CC2)n1) `ZINC000754535841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754535841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754535841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000754535841 none Cc1ccnc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 11, 50, 50, 11, 11, 11, 11, 7, 1, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 11, 11, 50, 50, 50, 50, 11, 50, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 11, 11, 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754535841 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000754535841 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754535841/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754535841/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754535841 Building ZINC000337274712 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337274712' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337274712 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337274712 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337274712/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337274712 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/341 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccncc1N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000337274712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337274712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337274712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000337274712 none Cc1ccncc1N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 9, 1, 14, 1, 1, 1, 7, 7, 7, 7, 7, 22, 22, 34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 7, 7, 22, 22, 22, 22] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 72 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337274712 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337274712/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337274712 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/342 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/342' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccncc1N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000337274712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337274712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337274712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000337274712 none Cc1ccncc1N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 23, 23, 23, 23, 9, 2, 14, 1, 1, 1, 7, 7, 7, 7, 7, 23, 23, 32, 32, 32, 32, 32, 32, 23, 23, 23, 23, 7, 7, 23, 23, 23, 23] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 69 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337274712 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337274712 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337274712/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337274712/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337274712 Building ZINC000337274712 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337274712' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337274712 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337274712 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337274712/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337274712 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 341) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccncc1N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000337274712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337274712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337274712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000337274712 none Cc1ccncc1N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 9, 1, 14, 1, 1, 1, 7, 7, 7, 7, 7, 22, 22, 34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 7, 7, 22, 22, 22, 22] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 72 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337274712 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337274712/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337274712 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 342) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccncc1N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000337274712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337274712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337274712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000337274712 none Cc1ccncc1N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 23, 23, 23, 23, 9, 2, 14, 1, 1, 1, 7, 7, 7, 7, 7, 23, 23, 32, 32, 32, 32, 32, 32, 23, 23, 23, 23, 7, 7, 23, 23, 23, 23] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 69 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337274712 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337274712 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337274712/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337274712/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337274712 Building ZINC000430081991 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430081991' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430081991 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430081991 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430081991/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430081991 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/343 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)ccc1OCCO) `ZINC000430081991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430081991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430081991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000430081991 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)ccc1OCCO NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', '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, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 4, 4, 17, 41, 41, 8, 8, 8, 8, 2, 5, 5, 8, 8, 41, 41, 41, 41, 123] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430081991 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430081991/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430081991 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/344 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/344' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)ccc1OCCO) `ZINC000430081991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430081991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430081991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000430081991 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)ccc1OCCO NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', '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, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 8, 24, 42, 42, 8, 8, 8, 8, 2, 5, 5, 8, 8, 42, 42, 42, 42, 126] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430081991 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430081991 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430081991/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430081991/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430081991 Building ZINC000430081991 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430081991' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430081991 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430081991 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430081991/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430081991 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 343) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)ccc1OCCO) `ZINC000430081991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430081991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430081991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000430081991 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)ccc1OCCO NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', '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, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 4, 4, 17, 41, 41, 8, 8, 8, 8, 2, 5, 5, 8, 8, 41, 41, 41, 41, 123] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430081991 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430081991/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430081991 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 344) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)ccc1OCCO) `ZINC000430081991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430081991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430081991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000430081991 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)ccc1OCCO NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', '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, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 8, 24, 42, 42, 8, 8, 8, 8, 2, 5, 5, 8, 8, 42, 42, 42, 42, 126] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430081991 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430081991 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430081991/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430081991/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430081991 Building ZINC000430092612 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092612' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092612 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430092612 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092612/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092612 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/345 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C/C=C/C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)OCC) `ZINC000430092612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430092612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000430092612 none C/C=C/C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 7, 2, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 7, 8, 8, 8, 19, 31, 31, 31, 31, 31, 20, 20, 2, 6, 6, 19, 19, 19, 19, 19] 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]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092612 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092612/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092612 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/346 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/346' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C/C=C/C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)OCC) `ZINC000430092612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430092612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000430092612 none C/C=C/C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 7, 2, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 7, 7, 7, 7, 20, 33, 33, 33, 33, 33, 20, 20, 2, 6, 6, 20, 20, 20, 20, 20] 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]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092612 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430092612 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092612/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092612/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092612 Building ZINC000430092612 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092612' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092612 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430092612 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092612/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092612 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 345) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C/C=C/C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)OCC) `ZINC000430092612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430092612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000430092612 none C/C=C/C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 7, 2, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 7, 8, 8, 8, 19, 31, 31, 31, 31, 31, 20, 20, 2, 6, 6, 19, 19, 19, 19, 19] 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]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092612 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092612/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092612 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 346) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C/C=C/C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)OCC) `ZINC000430092612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430092612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000430092612 none C/C=C/C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 7, 2, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 7, 7, 7, 7, 20, 33, 33, 33, 33, 33, 20, 20, 2, 6, 6, 20, 20, 20, 20, 20] 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]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092612 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430092612 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092612/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092612/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092612 Building ZINC000430092615 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092615' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092615 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430092615 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092615/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092615 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/347 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C/C=C/C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)OCC) `ZINC000430092615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430092615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000430092615 none C/C=C/C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 20, 7, 2, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 7, 8, 8, 8, 19, 32, 32, 32, 32, 32, 20, 20, 2, 6, 6, 19, 19, 19, 19, 19] 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]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092615 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092615/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092615 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/348 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/348' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C/C=C/C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)OCC) `ZINC000430092615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430092615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000430092615 none C/C=C/C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 20, 7, 2, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 7, 8, 8, 8, 19, 32, 32, 32, 32, 32, 20, 20, 2, 6, 6, 19, 19, 19, 19, 19] 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]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092615 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430092615 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092615/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092615/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092615 Building ZINC000430092615 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092615' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092615 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430092615 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092615/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092615 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 347) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C/C=C/C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)OCC) `ZINC000430092615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430092615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000430092615 none C/C=C/C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 20, 7, 2, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 7, 8, 8, 8, 19, 32, 32, 32, 32, 32, 20, 20, 2, 6, 6, 19, 19, 19, 19, 19] 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]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092615 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092615/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092615 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 348) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C/C=C/C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)OCC) `ZINC000430092615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430092615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000430092615 none C/C=C/C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 20, 7, 2, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 7, 8, 8, 8, 19, 32, 32, 32, 32, 32, 20, 20, 2, 6, 6, 19, 19, 19, 19, 19] 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]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092615 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430092615 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092615/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092615/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430092615 Building ZINC000428711008 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711008' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711008 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428711008 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711008/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711008 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/349 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccccc2)C1=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428711008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428711008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000428711008 none O=C(N[C@@H]1CCN(c2ccccc2)C1=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 9, 22, 22, 22, 22, 22, 27, 27, 22, 27, 27, 22, 22, 1, 1, 1, 10, 10, 10, 10, 10, 5, 22, 22, 22, 22, 27, 27, 25, 27, 27, 10, 10] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711008 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711008/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711008 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/350 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/350' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccccc2)C1=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428711008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428711008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000428711008 none O=C(N[C@@H]1CCN(c2ccccc2)C1=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 9, 24, 24, 24, 24, 24, 34, 34, 24, 34, 34, 24, 24, 1, 1, 1, 9, 9, 9, 9, 9, 5, 24, 24, 24, 24, 34, 34, 24, 34, 34, 9, 9] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711008 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428711008 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711008/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711008/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711008 Building ZINC000428711008 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711008' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711008 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428711008 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711008/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711008 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 349) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@@H]1CCN(c2ccccc2)C1=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428711008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428711008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000428711008 none O=C(N[C@@H]1CCN(c2ccccc2)C1=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 9, 22, 22, 22, 22, 22, 27, 27, 22, 27, 27, 22, 22, 1, 1, 1, 10, 10, 10, 10, 10, 5, 22, 22, 22, 22, 27, 27, 25, 27, 27, 10, 10] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711008 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711008/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711008 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 350) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@@H]1CCN(c2ccccc2)C1=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428711008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428711008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000428711008 none O=C(N[C@@H]1CCN(c2ccccc2)C1=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 9, 24, 24, 24, 24, 24, 34, 34, 24, 34, 34, 24, 24, 1, 1, 1, 9, 9, 9, 9, 9, 5, 24, 24, 24, 24, 34, 34, 24, 34, 34, 9, 9] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711008 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000428711008 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711008/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711008/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000428711008 Building ZINC000173033687 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173033687' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173033687 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173033687 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173033687/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173033687 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/351 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cnc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000173033687.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173033687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173033687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000173033687 none CCc1cnc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 15, 15, 15, 15, 9, 7, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 15, 29, 29, 29, 29, 29, 15, 9, 9, 7, 7, 2, 5, 5, 5, 5, 5, 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173033687 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173033687/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173033687 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/352 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/352' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cnc(CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000173033687.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173033687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173033687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000173033687 none CCc1cnc(CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 9, 7, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 16, 30, 30, 30, 30, 30, 16, 9, 9, 7, 7, 2, 4, 4, 4, 4, 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173033687 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000173033687 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173033687/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173033687/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173033687 Building ZINC000173033687 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173033687' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173033687 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173033687 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173033687/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173033687 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 351) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCc1cnc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000173033687.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173033687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173033687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000173033687 none CCc1cnc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 15, 15, 15, 15, 9, 7, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 15, 29, 29, 29, 29, 29, 15, 9, 9, 7, 7, 2, 5, 5, 5, 5, 5, 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173033687 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173033687/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173033687 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 352) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCc1cnc(CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000173033687.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173033687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173033687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000173033687 none CCc1cnc(CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 9, 7, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 16, 30, 30, 30, 30, 30, 16, 9, 9, 7, 7, 2, 4, 4, 4, 4, 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173033687 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000173033687 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173033687/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173033687/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173033687 Building ZINC000110397935 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000110397935' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000110397935 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000110397935 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000110397935/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000110397935 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/353 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/353' -> `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)Nc1ccccc1c1ccncc1) `ZINC000110397935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000110397935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000110397935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000110397935 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1c1ccncc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 36, 36, 36, 36, 36, 36, 44, 44, 36, 44, 44, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 36, 36, 36, 36, 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]) total number of confs: 97 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000110397935 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000110397935/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000110397935 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/354 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/354' -> `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)Nc1ccccc1c1ccncc1) `ZINC000110397935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000110397935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000110397935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000110397935 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1c1ccncc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 36, 36, 36, 36, 36, 36, 44, 44, 43, 44, 44, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 36, 36, 36, 36, 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]) total number of confs: 78 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000110397935 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000110397935 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000110397935/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000110397935/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000110397935 Building ZINC000110397935 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000110397935' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000110397935 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000110397935 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000110397935/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000110397935 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 353) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1c1ccncc1) `ZINC000110397935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000110397935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000110397935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000110397935 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1c1ccncc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 36, 36, 36, 36, 36, 36, 44, 44, 36, 44, 44, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 36, 36, 36, 36, 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]) total number of confs: 97 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000110397935 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000110397935/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000110397935 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 354) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1c1ccncc1) `ZINC000110397935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000110397935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000110397935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000110397935 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1c1ccncc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 36, 36, 36, 36, 36, 36, 44, 44, 43, 44, 44, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 36, 36, 36, 36, 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]) total number of confs: 78 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000110397935 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000110397935 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000110397935/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000110397935/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000110397935 Building ZINC000862677586 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677586' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677586 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000862677586 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677586/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677586 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/355 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C12CCC2) `ZINC000862677586.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000862677586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000862677586 none CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 35, 14, 35, 14, 14, 14, 5, 14, 3, 1, 3, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 124 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677586 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677586/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677586 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/356 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/356' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C12CCC2) `ZINC000862677586.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000862677586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677586/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000862677586 none CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 41, 20, 20, 20, 4, 20, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677586 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000862677586 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677586/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677586/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677586 Building ZINC000862677586 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677586' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677586 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000862677586 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677586/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677586 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 355) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C12CCC2) `ZINC000862677586.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000862677586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000862677586 none CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 35, 14, 35, 14, 14, 14, 5, 14, 3, 1, 3, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 124 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677586 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677586/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677586 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 356) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C12CCC2) `ZINC000862677586.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000862677586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677586/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000862677586 none CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 41, 20, 20, 20, 4, 20, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677586 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000862677586 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677586/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677586/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677586 Building ZINC000862677587 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677587' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677587 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000862677587 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677587/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677587 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/357 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C12CCC2) `ZINC000862677587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000862677587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000862677587 none CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 21, 43, 21, 21, 21, 6, 21, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677587 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677587/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677587 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/358 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/358' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C12CCC2) `ZINC000862677587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000862677587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000862677587 none CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 15, 34, 15, 15, 15, 7, 15, 3, 1, 3, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677587 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000862677587 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677587/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677587/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677587 Building ZINC000862677587 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677587' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677587 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000862677587 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677587/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677587 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 357) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C12CCC2) `ZINC000862677587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000862677587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000862677587 none CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 21, 43, 21, 21, 21, 6, 21, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677587 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677587/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677587 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 358) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C12CCC2) `ZINC000862677587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000862677587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000862677587 none CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 15, 34, 15, 15, 15, 7, 15, 3, 1, 3, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677587 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000862677587 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677587/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677587/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000862677587 Building ZINC000337290590 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000337290590 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/359 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/359' -> `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](c3ccccc3)C2)cn1) `ZINC000337290590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337290590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337290590 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[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', 'H', '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'] 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, 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, 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, 2, 10, 10, 10, 10, 10, 24, 24, 11, 24, 24, 10, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 10, 10, 24, 24, 24, 24, 24, 10, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/360 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/360' -> `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](c3ccccc3)C2)cn1) `ZINC000337290590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337290590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337290590 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[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', 'H', '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'] 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, 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, 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: [15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 25, 25, 11, 25, 25, 10, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 2, 10, 10, 25, 25, 25, 25, 25, 10, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/361 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/361' -> `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](c3ccccc3)C2)cn1) `ZINC000337290590.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000337290590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337290590 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[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', 'H', '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'] 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, 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, 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, 2, 10, 10, 10, 10, 10, 24, 24, 24, 24, 24, 10, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 10, 10, 24, 24, 24, 24, 24, 10, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/362 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/362' -> `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](c3ccccc3)C2)cn1) `ZINC000337290590.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000337290590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337290590 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[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', 'H', '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'] 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, 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, 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, 2, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 10, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 2, 10, 10, 25, 25, 25, 25, 25, 10, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337290590 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 Building ZINC000337290590 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000337290590 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 359) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccccc3)C2)cn1) `ZINC000337290590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337290590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337290590 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[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', 'H', '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'] 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, 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, 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, 2, 10, 10, 10, 10, 10, 24, 24, 11, 24, 24, 10, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 10, 10, 24, 24, 24, 24, 24, 10, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 360) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccccc3)C2)cn1) `ZINC000337290590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337290590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337290590 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[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', 'H', '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'] 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, 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, 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: [15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 25, 25, 11, 25, 25, 10, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 2, 10, 10, 25, 25, 25, 25, 25, 10, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 361) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](c3ccccc3)C2)cn1) `ZINC000337290590.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000337290590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337290590 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[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', 'H', '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'] 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, 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, 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, 2, 10, 10, 10, 10, 10, 24, 24, 24, 24, 24, 10, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 10, 10, 24, 24, 24, 24, 24, 10, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 362) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/362: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](c3ccccc3)C2)cn1) `ZINC000337290590.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000337290590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337290590 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[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', 'H', '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'] 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, 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, 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, 2, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 10, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 2, 10, 10, 25, 25, 25, 25, 25, 10, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337290590 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 Building ZINC000337290590 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000337290590 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 359) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccccc3)C2)cn1) `ZINC000337290590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337290590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337290590 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[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', 'H', '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'] 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, 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, 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, 2, 10, 10, 10, 10, 10, 24, 24, 11, 24, 24, 10, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 10, 10, 24, 24, 24, 24, 24, 10, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 360) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccccc3)C2)cn1) `ZINC000337290590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337290590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337290590 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[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', 'H', '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'] 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, 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, 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: [15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 25, 25, 11, 25, 25, 10, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 2, 10, 10, 25, 25, 25, 25, 25, 10, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 361) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](c3ccccc3)C2)cn1) `ZINC000337290590.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000337290590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337290590 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[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', 'H', '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'] 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, 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, 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, 2, 10, 10, 10, 10, 10, 24, 24, 24, 24, 24, 10, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 10, 10, 24, 24, 24, 24, 24, 10, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 362) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/362: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](c3ccccc3)C2)cn1) `ZINC000337290590.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000337290590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337290590 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[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', 'H', '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'] 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, 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, 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, 2, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 10, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 2, 10, 10, 25, 25, 25, 25, 25, 10, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337290590 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 Building ZINC000337290590 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000337290590 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 359) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccccc3)C2)cn1) `ZINC000337290590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337290590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337290590 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[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', 'H', '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'] 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, 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, 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, 2, 10, 10, 10, 10, 10, 24, 24, 11, 24, 24, 10, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 10, 10, 24, 24, 24, 24, 24, 10, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 360) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccccc3)C2)cn1) `ZINC000337290590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337290590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337290590 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[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', 'H', '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'] 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, 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, 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: [15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 25, 25, 11, 25, 25, 10, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 2, 10, 10, 25, 25, 25, 25, 25, 10, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 361) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](c3ccccc3)C2)cn1) `ZINC000337290590.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000337290590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337290590 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[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', 'H', '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'] 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, 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, 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, 2, 10, 10, 10, 10, 10, 24, 24, 24, 24, 24, 10, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 10, 10, 24, 24, 24, 24, 24, 10, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 362) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/362: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](c3ccccc3)C2)cn1) `ZINC000337290590.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000337290590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337290590 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[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', 'H', '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'] 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, 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, 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, 2, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 10, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 2, 10, 10, 25, 25, 25, 25, 25, 10, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337290590 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337290590 Building ZINC000173471879 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471879' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471879 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173471879 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471879/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471879 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/363 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000173471879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173471879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000173471879 none Cc1nn(C)c(C)c1C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', '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', 'Cl', '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, 8, 8, 5, 1, 5, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 34, 16, 4, 16, 16, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 16, 16, 16, 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, 38, 39, 40, 41, 42]) total number of confs: 179 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471879 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471879/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471879 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/364 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/364' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000173471879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173471879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000173471879 none Cc1nn(C)c(C)c1C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', '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', 'Cl', '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, 8, 8, 5, 1, 5, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 31, 12, 3, 12, 12, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 12, 12, 12, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 175 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471879 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000173471879 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471879/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471879/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471879 Building ZINC000173471879 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471879' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471879 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173471879 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471879/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471879 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 363) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(C)c1C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000173471879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173471879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000173471879 none Cc1nn(C)c(C)c1C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', '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', 'Cl', '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, 8, 8, 5, 1, 5, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 34, 16, 4, 16, 16, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 16, 16, 16, 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, 38, 39, 40, 41, 42]) total number of confs: 179 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471879 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471879/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471879 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 364) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(C)c1C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000173471879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173471879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000173471879 none Cc1nn(C)c(C)c1C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', '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', 'Cl', '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, 8, 8, 5, 1, 5, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 31, 12, 3, 12, 12, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 12, 12, 12, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 175 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471879 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000173471879 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471879/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471879/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471879 Building ZINC000173471889 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471889' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173471889 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471889/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/365 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000173471889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173471889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000173471889 none Cc1nn(C)c(C)c1C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', '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', 'Cl', '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, 8, 8, 5, 1, 5, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 31, 12, 3, 12, 12, 3, 1, 3, 1, 1, 1, 4, 4, 1, 1, 4, 4, 49, 49, 49, 49, 49, 49, 49, 49, 49, 31, 31, 12, 12, 12, 3, 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, 38, 39, 40, 41, 42]) total number of confs: 172 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471889/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/366 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/366' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000173471889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173471889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000173471889 none Cc1nn(C)c(C)c1C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', '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', 'Cl', '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, 8, 8, 5, 1, 5, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 33, 16, 4, 16, 16, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 16, 16, 16, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 179 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000173471889 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471889/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471889/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471889 Building ZINC000173471889 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471889' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173471889 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471889/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 365) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(C)c1C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000173471889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173471889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000173471889 none Cc1nn(C)c(C)c1C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', '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', 'Cl', '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, 8, 8, 5, 1, 5, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 31, 12, 3, 12, 12, 3, 1, 3, 1, 1, 1, 4, 4, 1, 1, 4, 4, 49, 49, 49, 49, 49, 49, 49, 49, 49, 31, 31, 12, 12, 12, 3, 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, 38, 39, 40, 41, 42]) total number of confs: 172 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471889/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 366) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(C)c1C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000173471889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173471889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000173471889 none Cc1nn(C)c(C)c1C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', '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', 'Cl', '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, 8, 8, 5, 1, 5, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 33, 16, 4, 16, 16, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 16, 16, 16, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 179 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000173471889 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471889/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471889/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000173471889 Building ZINC000754871650 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754871650' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754871650 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000754871650 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754871650/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754871650 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/367 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F) `ZINC000754871650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754871650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754871650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000754871650 none CN(C)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 11, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23, 11, 11, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 11] 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754871650 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754871650/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754871650 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/368 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/368' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F) `ZINC000754871650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754871650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754871650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000754871650 none CN(C)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 5, 10, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 10, 10, 2, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 10] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754871650 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000754871650 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754871650/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754871650/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754871650 Building ZINC000754871650 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754871650' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754871650 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000754871650 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754871650/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754871650 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 367) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN(C)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F) `ZINC000754871650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754871650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754871650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000754871650 none CN(C)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 11, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23, 11, 11, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 11] 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754871650 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754871650/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754871650 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 368) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN(C)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F) `ZINC000754871650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754871650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754871650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000754871650 none CN(C)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 5, 10, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 10, 10, 2, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 10] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754871650 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000754871650 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754871650/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754871650/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000754871650 Building ZINC000337297382 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297382' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337297382 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297382/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/369 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@H]1C(F)F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000337297382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337297382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000337297382 none O=C(N1CCCC[C@H]1C(F)F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 15, 15, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 11, 21, 21, 1, 1, 1, 7, 7, 7, 7, 16, 16, 7, 16, 16, 7, 11, 11, 11, 11, 11, 11, 11, 11, 21, 7, 16, 16, 7, 16, 16, 7] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297382/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/370 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/370' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@H]1C(F)F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000337297382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337297382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000337297382 none O=C(N1CCCC[C@H]1C(F)F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 15, 15, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 17, 17, 1, 1, 1, 6, 6, 6, 6, 17, 17, 6, 17, 17, 6, 7, 7, 7, 7, 7, 7, 7, 7, 17, 6, 17, 17, 6, 17, 17, 6] 36 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337297382 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297382/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297382/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297382 Building ZINC000337297382 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297382' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337297382 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297382/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 369) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCCC[C@H]1C(F)F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000337297382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337297382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000337297382 none O=C(N1CCCC[C@H]1C(F)F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 15, 15, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 11, 21, 21, 1, 1, 1, 7, 7, 7, 7, 16, 16, 7, 16, 16, 7, 11, 11, 11, 11, 11, 11, 11, 11, 21, 7, 16, 16, 7, 16, 16, 7] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297382/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 370) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCCC[C@H]1C(F)F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000337297382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337297382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000337297382 none O=C(N1CCCC[C@H]1C(F)F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 15, 15, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 17, 17, 1, 1, 1, 6, 6, 6, 6, 17, 17, 6, 17, 17, 6, 7, 7, 7, 7, 7, 7, 7, 7, 17, 6, 17, 17, 6, 17, 17, 6] 36 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337297382 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297382/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297382/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297382 Building ZINC000337297384 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297384' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297384 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337297384 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297384/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297384 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/371 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@@H]1C(F)F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000337297384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337297384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000337297384 none O=C(N1CCCC[C@@H]1C(F)F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 15, 15, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 4, 6, 6, 6, 6, 6, 6, 6, 15, 15, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 6, 15, 15, 15, 15, 15, 6] 31 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297384 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297384/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297384 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/372 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/372' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@@H]1C(F)F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000337297384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337297384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000337297384 none O=C(N1CCCC[C@@H]1C(F)F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 15, 15, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 11, 21, 21, 1, 1, 1, 7, 7, 7, 7, 16, 16, 7, 16, 16, 7, 11, 11, 11, 11, 11, 11, 11, 11, 21, 7, 16, 16, 7, 16, 16, 7] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297384 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337297384 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297384/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297384/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297384 Building ZINC000337297384 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297384' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297384 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337297384 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297384/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297384 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 371) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCCC[C@@H]1C(F)F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000337297384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337297384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000337297384 none O=C(N1CCCC[C@@H]1C(F)F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 15, 15, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 4, 6, 6, 6, 6, 6, 6, 6, 15, 15, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 6, 15, 15, 15, 15, 15, 6] 31 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297384 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297384/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297384 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 372) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCCC[C@@H]1C(F)F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000337297384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337297384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000337297384 none O=C(N1CCCC[C@@H]1C(F)F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 15, 15, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 11, 21, 21, 1, 1, 1, 7, 7, 7, 7, 16, 16, 7, 16, 16, 7, 11, 11, 11, 11, 11, 11, 11, 11, 21, 7, 16, 16, 7, 16, 16, 7] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297384 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337297384 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297384/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297384/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337297384 Building ZINC000337303382 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303382' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337303382 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303382/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/373 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](CO)CC1CCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000337303382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337303382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000337303382 none O=C(NC[C@@H](CO)CC1CCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 7, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 10, 25, 22, 26, 25, 30, 30, 30, 30, 30, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 26, 26, 78, 28, 28, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 222 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303382/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/374 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/374' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](CO)CC1CCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000337303382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337303382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000337303382 none O=C(NC[C@@H](CO)CC1CCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 7, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 11, 22, 20, 23, 22, 28, 28, 28, 28, 28, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 11, 11, 23, 23, 69, 26, 26, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 201 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337303382 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303382/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303382/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303382 Building ZINC000337303382 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303382' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337303382 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303382/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 373) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@@H](CO)CC1CCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000337303382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337303382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000337303382 none O=C(NC[C@@H](CO)CC1CCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 7, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 10, 25, 22, 26, 25, 30, 30, 30, 30, 30, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 26, 26, 78, 28, 28, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 222 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303382/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 374) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@@H](CO)CC1CCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000337303382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337303382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000337303382 none O=C(NC[C@@H](CO)CC1CCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 7, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 11, 22, 20, 23, 22, 28, 28, 28, 28, 28, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 11, 11, 23, 23, 69, 26, 26, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 201 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337303382 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303382/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303382/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303382 Building ZINC000337303383 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303383' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337303383 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303383/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/375 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](CO)CC1CCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000337303383.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337303383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000337303383 none O=C(NC[C@H](CO)CC1CCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 7, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 10, 20, 18, 21, 20, 29, 29, 29, 29, 29, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 21, 21, 63, 28, 28, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 212 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303383/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/376 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/376' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](CO)CC1CCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000337303383.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337303383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000337303383 none O=C(NC[C@H](CO)CC1CCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 7, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 8, 22, 20, 23, 22, 29, 31, 31, 31, 31, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 8, 8, 23, 23, 69, 28, 28, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 217 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337303383 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303383/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303383/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303383 Building ZINC000337303383 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303383' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337303383 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303383/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 375) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@H](CO)CC1CCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000337303383.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337303383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000337303383 none O=C(NC[C@H](CO)CC1CCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 7, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 10, 20, 18, 21, 20, 29, 29, 29, 29, 29, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 21, 21, 63, 28, 28, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 212 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303383/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 376) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@H](CO)CC1CCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000337303383.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337303383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000337303383 none O=C(NC[C@H](CO)CC1CCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 7, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 8, 22, 20, 23, 22, 29, 31, 31, 31, 31, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 8, 8, 23, 23, 69, 28, 28, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 217 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337303383 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303383/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303383/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337303383 Building ZINC000430257487 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257487' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257487 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430257487 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257487/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257487 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/377 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccsc1[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000430257487.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430257487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000430257487 none Cc1ccsc1[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 1, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 8, 5, 8, 8, 24, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 24, 24, 72, 5, 9, 9] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 193 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257487 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257487/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257487 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/378 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/378' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccsc1[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000430257487.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430257487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000430257487 none Cc1ccsc1[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 1, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 20, 8, 5, 8, 8, 26, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 26, 26, 78, 5, 8, 8] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 208 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257487 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430257487 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257487/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257487/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257487 Building ZINC000430257487 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257487' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257487 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430257487 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257487/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257487 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 377) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccsc1[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000430257487.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430257487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000430257487 none Cc1ccsc1[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 1, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 8, 5, 8, 8, 24, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 24, 24, 72, 5, 9, 9] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 193 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257487 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257487/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257487 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 378) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccsc1[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000430257487.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430257487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000430257487 none Cc1ccsc1[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 1, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 20, 8, 5, 8, 8, 26, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 26, 26, 78, 5, 8, 8] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 208 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257487 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430257487 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257487/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257487/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257487 Building ZINC000430257493 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257493' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257493 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430257493 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257493/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257493 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/379 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccsc1[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000430257493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430257493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000430257493 none Cc1ccsc1[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 1, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 20, 8, 5, 8, 8, 26, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 26, 26, 78, 5, 8, 8] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 208 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257493 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257493/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257493 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/380 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/380' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccsc1[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000430257493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430257493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000430257493 none Cc1ccsc1[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 1, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 8, 5, 8, 8, 25, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 25, 25, 75, 5, 9, 9] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 199 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257493 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430257493 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257493/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257493/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257493 Building ZINC000430257493 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257493' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257493 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430257493 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257493/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257493 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 379) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccsc1[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000430257493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430257493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000430257493 none Cc1ccsc1[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 1, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 20, 8, 5, 8, 8, 26, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 26, 26, 78, 5, 8, 8] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 208 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257493 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257493/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257493 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 380) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccsc1[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000430257493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430257493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000430257493 none Cc1ccsc1[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 1, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 8, 5, 8, 8, 25, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 25, 25, 75, 5, 9, 9] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 199 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257493 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430257493 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257493/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257493/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430257493 Building ZINC000430275177 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430275177' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430275177 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430275177 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430275177/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430275177 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/381 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(CO)c(F)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000430275177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430275177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430275177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000430275177 none O=C(NCc1ccc(CO)c(F)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 12, 1, 15, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 12, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 3, 3, 3, 3, 3, 2, 12, 12, 48, 48, 48, 48, 144, 48, 3, 3] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430275177 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430275177/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430275177 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/382 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/382' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(CO)c(F)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000430275177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430275177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430275177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000430275177 none O=C(NCc1ccc(CO)c(F)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 12, 1, 15, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 12, 48, 48, 48, 48, 48, 48, 48, 43, 1, 1, 1, 3, 3, 3, 3, 3, 2, 12, 12, 48, 48, 48, 48, 144, 48, 3, 3] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430275177 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430275177 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430275177/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430275177/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430275177 Building ZINC000430275177 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430275177' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430275177 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430275177 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430275177/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430275177 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 381) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NCc1ccc(CO)c(F)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000430275177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430275177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430275177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000430275177 none O=C(NCc1ccc(CO)c(F)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 12, 1, 15, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 12, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 3, 3, 3, 3, 3, 2, 12, 12, 48, 48, 48, 48, 144, 48, 3, 3] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430275177 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430275177/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430275177 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 382) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NCc1ccc(CO)c(F)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000430275177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430275177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430275177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000430275177 none O=C(NCc1ccc(CO)c(F)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 12, 1, 15, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 12, 48, 48, 48, 48, 48, 48, 48, 43, 1, 1, 1, 3, 3, 3, 3, 3, 2, 12, 12, 48, 48, 48, 48, 144, 48, 3, 3] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430275177 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430275177 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430275177/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430275177/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430275177 Building ZINC000430276586 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276586' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276586 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430276586 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276586/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276586 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/383 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1nc[nH]n1)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000430276586.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430276586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000430276586 none O=C(N[C@@H](c1nc[nH]n1)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 8, 1, 8, 6, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 4, 6, 6, 23, 23, 23, 23, 23, 6, 12, 12, 6, 12, 12, 1, 1, 1, 9, 9, 9, 9, 9, 4, 23, 12, 12, 6, 12, 12, 9, 9] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 80 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276586 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276586/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276586 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/384 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/384' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1nc[nH]n1)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000430276586.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430276586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276586/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000430276586 none O=C(N[C@@H](c1nc[nH]n1)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 8, 1, 8, 6, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 4, 6, 6, 25, 25, 25, 25, 25, 6, 13, 13, 6, 13, 13, 1, 1, 1, 8, 8, 8, 8, 8, 4, 25, 13, 13, 9, 13, 13, 8, 8] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 89 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276586 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430276586 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276586/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276586/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276586 Building ZINC000430276586 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276586' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276586 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430276586 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276586/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276586 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 383) grep: /scratch/xiaobo/83235/xao-8058115.15/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(N[C@@H](c1nc[nH]n1)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000430276586.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430276586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000430276586 none O=C(N[C@@H](c1nc[nH]n1)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 8, 1, 8, 6, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 4, 6, 6, 23, 23, 23, 23, 23, 6, 12, 12, 6, 12, 12, 1, 1, 1, 9, 9, 9, 9, 9, 4, 23, 12, 12, 6, 12, 12, 9, 9] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 80 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276586 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276586/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276586 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 384) grep: /scratch/xiaobo/83235/xao-8058115.15/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(N[C@@H](c1nc[nH]n1)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000430276586.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430276586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276586/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000430276586 none O=C(N[C@@H](c1nc[nH]n1)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 8, 1, 8, 6, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 4, 6, 6, 25, 25, 25, 25, 25, 6, 13, 13, 6, 13, 13, 1, 1, 1, 8, 8, 8, 8, 8, 4, 25, 13, 13, 9, 13, 13, 8, 8] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 89 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276586 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430276586 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276586/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276586/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276586 Building ZINC000430276587 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276587' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276587 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430276587 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276587/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276587 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/385 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1nc[nH]n1)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000430276587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430276587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000430276587 none O=C(N[C@H](c1nc[nH]n1)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 8, 1, 8, 6, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 4, 7, 7, 26, 26, 26, 26, 26, 7, 14, 14, 7, 14, 14, 1, 1, 1, 8, 8, 8, 8, 8, 4, 26, 14, 14, 7, 14, 14, 8, 8] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 89 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276587 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276587/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276587 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/386 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/386' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1nc[nH]n1)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000430276587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430276587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000430276587 none O=C(N[C@H](c1nc[nH]n1)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 8, 1, 8, 6, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 4, 6, 6, 23, 23, 23, 23, 23, 6, 12, 12, 6, 12, 12, 1, 1, 1, 9, 9, 9, 9, 9, 4, 23, 12, 12, 6, 12, 12, 9, 9] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 80 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276587 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430276587 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276587/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276587/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276587 Building ZINC000430276587 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276587' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276587 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430276587 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276587/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276587 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 385) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H](c1nc[nH]n1)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000430276587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430276587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000430276587 none O=C(N[C@H](c1nc[nH]n1)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 8, 1, 8, 6, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 4, 7, 7, 26, 26, 26, 26, 26, 7, 14, 14, 7, 14, 14, 1, 1, 1, 8, 8, 8, 8, 8, 4, 26, 14, 14, 7, 14, 14, 8, 8] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 89 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276587 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276587/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276587 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 386) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H](c1nc[nH]n1)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000430276587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430276587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000430276587 none O=C(N[C@H](c1nc[nH]n1)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 8, 1, 8, 6, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 4, 6, 6, 23, 23, 23, 23, 23, 6, 12, 12, 6, 12, 12, 1, 1, 1, 9, 9, 9, 9, 9, 4, 23, 12, 12, 6, 12, 12, 9, 9] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 80 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276587 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430276587 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276587/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276587/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430276587 Building ZINC000430288194 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430288194' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430288194 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430288194 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430288194/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430288194 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/387 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cc1CO) `ZINC000430288194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430288194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430288194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000430288194 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cc1CO NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.3', 'O.3', '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, 16, 14, 1, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 2, 2, 10, 10, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 10, 10, 10, 29, 22, 22, 22, 10, 10, 2, 7, 7, 10, 29, 29, 87] 150 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]) total number of confs: 244 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430288194 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430288194/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430288194 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/388 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/388' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cc1CO) `ZINC000430288194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430288194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430288194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000430288194 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cc1CO NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.3', 'O.3', '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, 16, 14, 1, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 2, 2, 9, 9, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 9, 9, 9, 28, 15, 15, 15, 9, 9, 2, 7, 7, 9, 28, 28, 84] 150 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]) total number of confs: 212 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430288194 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430288194 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430288194/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430288194/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430288194 Building ZINC000430288194 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430288194' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430288194 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430288194 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430288194/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430288194 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 387) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cc1CO) `ZINC000430288194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430288194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430288194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000430288194 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cc1CO NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.3', 'O.3', '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, 16, 14, 1, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 2, 2, 10, 10, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 10, 10, 10, 29, 22, 22, 22, 10, 10, 2, 7, 7, 10, 29, 29, 87] 150 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]) total number of confs: 244 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430288194 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430288194/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430288194 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 388) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cc1CO) `ZINC000430288194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430288194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430288194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000430288194 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cc1CO NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.3', 'O.3', '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, 16, 14, 1, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 2, 2, 9, 9, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 9, 9, 9, 28, 15, 15, 15, 9, 9, 2, 7, 7, 9, 28, 28, 84] 150 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]) total number of confs: 212 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430288194 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430288194 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430288194/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430288194/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430288194 Building ZINC000430305763 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305763' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305763 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430305763 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305763/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305763 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/389 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)Cc1ccccc1) `ZINC000430305763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430305763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000430305763 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 11, 5, 1, 1, 1, 1, 1, 1, 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, 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, 2, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 26, 26, 44, 44, 44, 44, 44, 44, 6, 6, 6, 2, 6, 6, 44, 44, 44, 44, 44, 44, 44] 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305763 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305763/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305763 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/390 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/390' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)Cc1ccccc1) `ZINC000430305763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430305763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000430305763 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 11, 5, 1, 1, 1, 1, 1, 1, 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, 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, 2, 6, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 6, 24, 24, 43, 43, 43, 43, 43, 43, 6, 6, 6, 2, 5, 5, 43, 43, 43, 43, 43, 43, 43] 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305763 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430305763 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305763/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305763/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305763 Building ZINC000430305763 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305763' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305763 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430305763 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305763/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305763 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 389) grep: /scratch/xiaobo/83235/xao-8058115.15/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](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)Cc1ccccc1) `ZINC000430305763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430305763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000430305763 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 11, 5, 1, 1, 1, 1, 1, 1, 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, 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, 2, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 26, 26, 44, 44, 44, 44, 44, 44, 6, 6, 6, 2, 6, 6, 44, 44, 44, 44, 44, 44, 44] 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305763 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305763/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305763 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 390) grep: /scratch/xiaobo/83235/xao-8058115.15/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](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)Cc1ccccc1) `ZINC000430305763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430305763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000430305763 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 11, 5, 1, 1, 1, 1, 1, 1, 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, 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, 2, 6, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 6, 24, 24, 43, 43, 43, 43, 43, 43, 6, 6, 6, 2, 5, 5, 43, 43, 43, 43, 43, 43, 43] 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305763 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430305763 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305763/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305763/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305763 Building ZINC000430305764 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305764' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305764 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430305764 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305764/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305764 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/391 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)Cc1ccccc1) `ZINC000430305764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430305764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000430305764 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 11, 5, 1, 1, 1, 1, 1, 1, 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, 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, 2, 6, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 6, 24, 24, 43, 43, 43, 43, 43, 43, 6, 6, 6, 2, 5, 5, 43, 43, 43, 43, 43, 43, 43] 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305764 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305764/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305764 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/392 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/392' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)Cc1ccccc1) `ZINC000430305764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430305764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000430305764 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 11, 5, 1, 1, 1, 1, 1, 1, 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, 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, 2, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 26, 26, 45, 45, 45, 45, 45, 45, 6, 6, 6, 2, 6, 6, 45, 45, 45, 45, 45, 45, 45] 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]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305764 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430305764 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305764/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305764/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305764 Building ZINC000430305764 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305764' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305764 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430305764 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305764/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305764 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 391) grep: /scratch/xiaobo/83235/xao-8058115.15/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](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)Cc1ccccc1) `ZINC000430305764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430305764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000430305764 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 11, 5, 1, 1, 1, 1, 1, 1, 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, 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, 2, 6, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 6, 24, 24, 43, 43, 43, 43, 43, 43, 6, 6, 6, 2, 5, 5, 43, 43, 43, 43, 43, 43, 43] 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305764 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305764/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305764 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 392) grep: /scratch/xiaobo/83235/xao-8058115.15/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](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)Cc1ccccc1) `ZINC000430305764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430305764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000430305764 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(=O)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 11, 5, 1, 1, 1, 1, 1, 1, 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, 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, 2, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 26, 26, 45, 45, 45, 45, 45, 45, 6, 6, 6, 2, 6, 6, 45, 45, 45, 45, 45, 45, 45] 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]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305764 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430305764 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305764/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305764/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430305764 Building ZINC000337319843 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337319843' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337319843 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337319843 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337319843/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337319843 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/393 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/393' -> `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(F)(F)CC2)cn1) `ZINC000337319843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337319843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337319843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337319843 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC2CCC(F)(F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 25, 25, 25, 25, 25, 25, 25, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 2, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337319843 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337319843/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337319843 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/394 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/394' -> `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(F)(F)CC2)cn1) `ZINC000337319843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337319843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337319843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337319843 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC2CCC(F)(F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 2, 2, 2, 14, 26, 26, 26, 26, 26, 26, 26, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 2, 14, 14, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337319843 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337319843 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337319843/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337319843/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337319843 Building ZINC000337319843 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337319843' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337319843 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337319843 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337319843/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337319843 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 393) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC2CCC(F)(F)CC2)cn1) `ZINC000337319843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337319843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337319843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337319843 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC2CCC(F)(F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 25, 25, 25, 25, 25, 25, 25, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 2, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337319843 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337319843/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337319843 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 394) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC2CCC(F)(F)CC2)cn1) `ZINC000337319843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337319843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337319843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337319843 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC2CCC(F)(F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 2, 2, 2, 14, 26, 26, 26, 26, 26, 26, 26, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 2, 14, 14, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337319843 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337319843 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337319843/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337319843/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337319843 Building ZINC000430378950 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378950' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378950 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430378950 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378950/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378950 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/395 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ccnc1[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000430378950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430378950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000430378950 none CCn1ccnc1[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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.ar', 'C.ar', 'C.ar', 'C.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, 5, 8, 1, 1, 8, 1, 5, 7, 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] 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] 0 hydrogens need 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, 25, 25, 25, 25, 25, 25, 25, 17, 3, 17, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 45, 45, 25, 25, 25, 25, 25, 25, 25, 25, 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: 121 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378950 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378950/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378950 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/396 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/396' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ccnc1[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000430378950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430378950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000430378950 none CCn1ccnc1[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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.ar', 'C.ar', 'C.ar', 'C.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, 5, 8, 1, 1, 8, 1, 5, 7, 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] 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] 0 hydrogens 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, 45, 45, 45, 45, 45, 26, 26, 26, 26, 26, 26, 26, 20, 2, 20, 1, 1, 1, 4, 4, 1, 1, 4, 4, 49, 49, 49, 49, 49, 45, 45, 26, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 120 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378950 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430378950 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378950/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378950/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378950 Building ZINC000430378950 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378950' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378950 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430378950 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378950/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378950 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 395) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCn1ccnc1[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000430378950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430378950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000430378950 none CCn1ccnc1[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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.ar', 'C.ar', 'C.ar', 'C.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, 5, 8, 1, 1, 8, 1, 5, 7, 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] 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] 0 hydrogens need 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, 25, 25, 25, 25, 25, 25, 25, 17, 3, 17, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 45, 45, 25, 25, 25, 25, 25, 25, 25, 25, 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: 121 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378950 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378950/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378950 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 396) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCn1ccnc1[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000430378950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430378950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000430378950 none CCn1ccnc1[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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.ar', 'C.ar', 'C.ar', 'C.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, 5, 8, 1, 1, 8, 1, 5, 7, 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] 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] 0 hydrogens 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, 45, 45, 45, 45, 45, 26, 26, 26, 26, 26, 26, 26, 20, 2, 20, 1, 1, 1, 4, 4, 1, 1, 4, 4, 49, 49, 49, 49, 49, 45, 45, 26, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 120 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378950 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430378950 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378950/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378950/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378950 Building ZINC000430378951 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378951' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378951 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430378951 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378951/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378951 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/397 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ccnc1[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000430378951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430378951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000430378951 none CCn1ccnc1[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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.ar', 'C.ar', 'C.ar', 'C.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, 5, 8, 1, 1, 8, 1, 5, 7, 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] 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] 0 hydrogens need 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, 25, 25, 25, 25, 25, 25, 25, 19, 2, 19, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 45, 45, 25, 25, 25, 25, 25, 25, 25, 25, 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: 120 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378951 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378951/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378951 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/398 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/398' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ccnc1[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000430378951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430378951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000430378951 none CCn1ccnc1[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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.ar', 'C.ar', 'C.ar', 'C.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, 5, 8, 1, 1, 8, 1, 5, 7, 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] 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] 0 hydrogens need 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, 27, 27, 27, 27, 27, 27, 27, 19, 2, 19, 1, 1, 1, 4, 4, 1, 1, 4, 4, 50, 50, 50, 50, 50, 45, 45, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378951 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430378951 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378951/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378951/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378951 Building ZINC000430378951 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378951' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378951 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430378951 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378951/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378951 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 397) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCn1ccnc1[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000430378951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430378951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000430378951 none CCn1ccnc1[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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.ar', 'C.ar', 'C.ar', 'C.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, 5, 8, 1, 1, 8, 1, 5, 7, 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] 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] 0 hydrogens need 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, 25, 25, 25, 25, 25, 25, 25, 19, 2, 19, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 45, 45, 25, 25, 25, 25, 25, 25, 25, 25, 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: 120 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378951 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378951/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378951 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 398) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCn1ccnc1[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000430378951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430378951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000430378951 none CCn1ccnc1[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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.ar', 'C.ar', 'C.ar', 'C.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, 5, 8, 1, 1, 8, 1, 5, 7, 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] 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] 0 hydrogens need 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, 27, 27, 27, 27, 27, 27, 27, 19, 2, 19, 1, 1, 1, 4, 4, 1, 1, 4, 4, 50, 50, 50, 50, 50, 45, 45, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378951 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430378951 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378951/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378951/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430378951 Building ZINC000430532904 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430532904' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430532904 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430532904 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430532904/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430532904 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/399 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(C(C)(C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)s1) `ZINC000430532904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430532904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430532904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000430532904 none Cc1cnc(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', 'C.2', 'N.2', 'C.2', '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', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 17, 17, 17, 6, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 4, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430532904 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430532904/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430532904 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/400 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/400' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(C(C)(C)NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)s1) `ZINC000430532904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430532904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430532904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000430532904 none Cc1cnc(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', 'C.2', 'N.2', 'C.2', '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', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 4, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430532904 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430532904 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430532904/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430532904/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430532904 Building ZINC000430532904 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430532904' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430532904 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000430532904 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430532904/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430532904 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 399) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1cnc(C(C)(C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)s1) `ZINC000430532904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000430532904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430532904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000430532904 none Cc1cnc(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', 'C.2', 'N.2', 'C.2', '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', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 17, 17, 17, 6, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 4, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430532904 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430532904/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430532904 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 400) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1cnc(C(C)(C)NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)s1) `ZINC000430532904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000430532904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430532904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000430532904 none Cc1cnc(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', 'C.2', 'N.2', 'C.2', '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', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 4, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430532904 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000430532904 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430532904/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430532904/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000430532904 Building ZINC000175100675 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100675' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175100675 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100675/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/401 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](O)c1ccc(Cl)s1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000175100675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175100675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000175100675 none O=C(NC[C@H](O)c1ccc(Cl)s1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 1, 1, 1, 1, 16, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 12, 21, 21, 21, 29, 29, 29, 29, 29, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 63, 29, 29, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100675/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/402 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/402' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](O)c1ccc(Cl)s1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000175100675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175100675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000175100675 none O=C(NC[C@H](O)c1ccc(Cl)s1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 1, 1, 1, 1, 16, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 13, 22, 22, 22, 30, 30, 30, 30, 30, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 66, 30, 30, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 176 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175100675 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100675/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100675/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100675 Building ZINC000175100675 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100675' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175100675 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100675/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 401) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@H](O)c1ccc(Cl)s1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000175100675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175100675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000175100675 none O=C(NC[C@H](O)c1ccc(Cl)s1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 1, 1, 1, 1, 16, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 12, 21, 21, 21, 29, 29, 29, 29, 29, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 63, 29, 29, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100675/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 402) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@H](O)c1ccc(Cl)s1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000175100675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175100675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000175100675 none O=C(NC[C@H](O)c1ccc(Cl)s1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 1, 1, 1, 1, 16, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 13, 22, 22, 22, 30, 30, 30, 30, 30, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 66, 30, 30, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 176 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175100675 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100675/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100675/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100675 Building ZINC000175100694 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100694' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100694 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175100694 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100694/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100694 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/403 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](O)c1ccc(Cl)s1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000175100694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175100694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000175100694 none O=C(NC[C@@H](O)c1ccc(Cl)s1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 1, 1, 1, 1, 16, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 13, 22, 22, 22, 30, 30, 30, 30, 30, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 66, 30, 30, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 176 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100694 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100694/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100694 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/404 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/404' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](O)c1ccc(Cl)s1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000175100694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175100694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000175100694 none O=C(NC[C@@H](O)c1ccc(Cl)s1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 1, 1, 1, 1, 16, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 11, 20, 20, 20, 28, 28, 28, 28, 28, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 11, 11, 60, 28, 28, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 166 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100694 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175100694 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100694/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100694/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100694 Building ZINC000175100694 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100694' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100694 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175100694 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100694/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100694 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 403) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NC[C@@H](O)c1ccc(Cl)s1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000175100694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175100694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000175100694 none O=C(NC[C@@H](O)c1ccc(Cl)s1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 1, 1, 1, 1, 16, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 13, 22, 22, 22, 30, 30, 30, 30, 30, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 66, 30, 30, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 176 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100694 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100694/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100694 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 404) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NC[C@@H](O)c1ccc(Cl)s1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000175100694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175100694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000175100694 none O=C(NC[C@@H](O)c1ccc(Cl)s1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 1, 1, 1, 1, 16, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 11, 20, 20, 20, 28, 28, 28, 28, 28, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 11, 11, 60, 28, 28, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 166 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100694 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175100694 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100694/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100694/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175100694 Building ZINC000175107334 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175107334' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175107334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175107334 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175107334/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175107334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/405 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1nc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)cc3)ccc2o1) `ZINC000175107334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175107334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175107334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000175107334 none COCc1nc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)cc3)ccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 11, 11, 11, 11, 50, 50, 50, 43, 43, 11, 2, 2, 2, 4, 4, 4, 2, 2, 11, 11] 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: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175107334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175107334/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175107334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/406 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/406' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1nc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)cc3)ccc2o1) `ZINC000175107334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175107334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175107334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000175107334 none COCc1nc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)cc3)ccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 11, 11, 11, 11, 50, 50, 50, 43, 43, 11, 2, 2, 2, 4, 4, 4, 2, 2, 11, 11] 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: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175107334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175107334 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175107334/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175107334/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175107334 Building ZINC000175107334 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175107334' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175107334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175107334 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175107334/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175107334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 405) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COCc1nc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)cc3)ccc2o1) `ZINC000175107334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175107334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175107334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000175107334 none COCc1nc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)cc3)ccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 11, 11, 11, 11, 50, 50, 50, 43, 43, 11, 2, 2, 2, 4, 4, 4, 2, 2, 11, 11] 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: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175107334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175107334/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175107334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 406) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COCc1nc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)cc3)ccc2o1) `ZINC000175107334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175107334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175107334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000175107334 none COCc1nc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)cc3)ccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 11, 11, 11, 11, 50, 50, 50, 43, 43, 11, 2, 2, 2, 4, 4, 4, 2, 2, 11, 11] 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: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175107334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175107334 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175107334/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175107334/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175107334 Building ZINC000175149030 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149030' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149030 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175149030 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149030/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149030 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/407 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000175149030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175149030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000175149030 none Cc1nccn1C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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', '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, 1, 8, 1, 1, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 16, 16, 16, 16, 16, 16, 9, 1, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 38, 38, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 164 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149030 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149030/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149030 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/408 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/408' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000175149030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175149030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000175149030 none Cc1nccn1C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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', '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, 1, 8, 1, 1, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations 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, 14, 14, 14, 14, 14, 14, 9, 1, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 35, 35, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 154 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149030 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175149030 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149030/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149030/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149030 Building ZINC000175149030 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149030' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149030 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175149030 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149030/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149030 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 407) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nccn1C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000175149030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175149030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000175149030 none Cc1nccn1C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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', '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, 1, 8, 1, 1, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 16, 16, 16, 16, 16, 16, 9, 1, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 38, 38, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 164 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149030 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149030/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149030 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 408) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nccn1C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000175149030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175149030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000175149030 none Cc1nccn1C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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', '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, 1, 8, 1, 1, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations 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, 14, 14, 14, 14, 14, 14, 9, 1, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 35, 35, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 154 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149030 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175149030 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149030/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149030/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149030 Building ZINC000175149048 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149048' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149048 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175149048 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149048/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149048 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/409 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000175149048.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175149048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000175149048 none Cc1nccn1C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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', '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, 1, 8, 1, 1, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations 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, 14, 14, 14, 14, 14, 14, 9, 1, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 35, 35, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 154 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149048 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149048/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149048 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/410 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/410' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000175149048.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175149048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149048/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000175149048 none Cc1nccn1C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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', '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, 1, 8, 1, 1, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 16, 16, 16, 16, 16, 16, 9, 1, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 38, 38, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 164 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149048 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175149048 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149048/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149048/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149048 Building ZINC000175149048 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149048' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149048 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175149048 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149048/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149048 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 409) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nccn1C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000175149048.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175149048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000175149048 none Cc1nccn1C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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', '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, 1, 8, 1, 1, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations 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, 14, 14, 14, 14, 14, 14, 9, 1, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 35, 35, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 154 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149048 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149048/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149048 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 410) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nccn1C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000175149048.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175149048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149048/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000175149048 none Cc1nccn1C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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', '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, 1, 8, 1, 1, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 16, 16, 16, 16, 16, 16, 9, 1, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 38, 38, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 164 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149048 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175149048 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149048/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149048/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175149048 Building ZINC000927124739 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927124739' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927124739 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927124739 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927124739/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927124739 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/411 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(C(=O)OC(C)(C)C)C[C@H]1C) `ZINC000927124739.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927124739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927124739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000927124739 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(C(=O)OC(C)(C)C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 12, 14, 14, 14, 14, 18, 18, 18, 18, 18, 18, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 7, 7, 14, 14, 18, 18, 18, 18, 18, 18, 18, 18, 18, 14, 14, 14, 14, 14] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 37] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927124739 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927124739/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927124739 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/412 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/412' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(C(=O)OC(C)(C)C)C[C@H]1C) `ZINC000927124739.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927124739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927124739/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000927124739 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(C(=O)OC(C)(C)C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 11, 14, 14, 14, 14, 19, 19, 19, 19, 19, 19, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 7, 7, 14, 14, 19, 19, 19, 19, 19, 19, 19, 19, 19, 14, 14, 14, 14, 14] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 37] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927124739 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000927124739 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927124739/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927124739/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927124739 Building ZINC000927124739 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927124739' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927124739 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927124739 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927124739/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927124739 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 411) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(C(=O)OC(C)(C)C)C[C@H]1C) `ZINC000927124739.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927124739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927124739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000927124739 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(C(=O)OC(C)(C)C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 12, 14, 14, 14, 14, 18, 18, 18, 18, 18, 18, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 7, 7, 14, 14, 18, 18, 18, 18, 18, 18, 18, 18, 18, 14, 14, 14, 14, 14] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 37] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927124739 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927124739/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927124739 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 412) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(C(=O)OC(C)(C)C)C[C@H]1C) `ZINC000927124739.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927124739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927124739/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000927124739 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(C(=O)OC(C)(C)C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 11, 14, 14, 14, 14, 19, 19, 19, 19, 19, 19, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 7, 7, 14, 14, 19, 19, 19, 19, 19, 19, 19, 19, 19, 14, 14, 14, 14, 14] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 37] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927124739 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000927124739 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927124739/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927124739/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000927124739 Building ZINC000175169058 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000175169058 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/413 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@](CCC(C)C)CC2)cc1) `ZINC000175169058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175169058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000175169058 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@](CCC(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 15, 25, 25, 25, 25, 25, 46, 50, 50, 50, 25, 25, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 25, 25, 25, 25, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/414 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/414' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@@](CCC(C)C)CC2)cc1) `ZINC000175169058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175169058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000175169058 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@@](CCC(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 15, 25, 25, 25, 25, 25, 46, 50, 50, 50, 25, 25, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 25, 25, 25, 25, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/415 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/415' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@](CCC(C)C)CC2)cc1) `ZINC000175169058.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000175169058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000175169058 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@](CCC(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 15, 25, 25, 25, 25, 25, 46, 50, 50, 50, 25, 25, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 25, 25, 25, 25, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/416 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/416' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@@](CCC(C)C)CC2)cc1) `ZINC000175169058.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000175169058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000175169058 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@@](CCC(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 15, 25, 25, 25, 25, 25, 46, 50, 50, 50, 25, 25, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 25, 25, 25, 25, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175169058 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 Building ZINC000175169058 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000175169058 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 413) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@](CCC(C)C)CC2)cc1) `ZINC000175169058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175169058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000175169058 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@](CCC(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 15, 25, 25, 25, 25, 25, 46, 50, 50, 50, 25, 25, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 25, 25, 25, 25, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 414) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@@](CCC(C)C)CC2)cc1) `ZINC000175169058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175169058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000175169058 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@@](CCC(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 15, 25, 25, 25, 25, 25, 46, 50, 50, 50, 25, 25, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 25, 25, 25, 25, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 415) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/415: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@](CCC(C)C)CC2)cc1) `ZINC000175169058.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000175169058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000175169058 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@](CCC(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 15, 25, 25, 25, 25, 25, 46, 50, 50, 50, 25, 25, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 25, 25, 25, 25, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 416) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@@](CCC(C)C)CC2)cc1) `ZINC000175169058.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000175169058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000175169058 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@@](CCC(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 15, 25, 25, 25, 25, 25, 46, 50, 50, 50, 25, 25, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 25, 25, 25, 25, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175169058 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 Building ZINC000175169058 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000175169058 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 413) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@](CCC(C)C)CC2)cc1) `ZINC000175169058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175169058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000175169058 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@](CCC(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 15, 25, 25, 25, 25, 25, 46, 50, 50, 50, 25, 25, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 25, 25, 25, 25, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 414) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@@](CCC(C)C)CC2)cc1) `ZINC000175169058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175169058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000175169058 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@@](CCC(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 15, 25, 25, 25, 25, 25, 46, 50, 50, 50, 25, 25, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 25, 25, 25, 25, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 415) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/415: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@](CCC(C)C)CC2)cc1) `ZINC000175169058.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000175169058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000175169058 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@](CCC(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 15, 25, 25, 25, 25, 25, 46, 50, 50, 50, 25, 25, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 25, 25, 25, 25, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 416) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@@](CCC(C)C)CC2)cc1) `ZINC000175169058.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000175169058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000175169058 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@@](CCC(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 15, 25, 25, 25, 25, 25, 46, 50, 50, 50, 25, 25, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 25, 25, 25, 25, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175169058 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 Building ZINC000175169058 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000175169058 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 413) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@](CCC(C)C)CC2)cc1) `ZINC000175169058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175169058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000175169058 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@](CCC(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 15, 25, 25, 25, 25, 25, 46, 50, 50, 50, 25, 25, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 25, 25, 25, 25, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 414) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@@](CCC(C)C)CC2)cc1) `ZINC000175169058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175169058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000175169058 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@@](CCC(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 15, 25, 25, 25, 25, 25, 46, 50, 50, 50, 25, 25, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 25, 25, 25, 25, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 415) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/415: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@](CCC(C)C)CC2)cc1) `ZINC000175169058.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000175169058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000175169058 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@](CCC(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 15, 25, 25, 25, 25, 25, 46, 50, 50, 50, 25, 25, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 25, 25, 25, 25, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 416) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@@](CCC(C)C)CC2)cc1) `ZINC000175169058.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000175169058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000175169058 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[N@@](CCC(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 15, 25, 25, 25, 25, 25, 46, 50, 50, 50, 25, 25, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 25, 25, 25, 25, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175169058 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175169058 Building ZINC000681706828 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000681706828' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000681706828 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000681706828 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000681706828/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000681706828 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/417 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Oc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccn1) `ZINC000681706828.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000681706828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000681706828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000681706828 none CC(C)Oc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 20, 30, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 8, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 8, 8] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000681706828 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000681706828/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000681706828 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/418 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/418' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Oc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccn1) `ZINC000681706828.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000681706828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000681706828/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000681706828 none CC(C)Oc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 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, 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] 0 hydrogens 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, 23, 31, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 8, 8, 8, 31, 31, 31, 31, 31, 31, 31, 8, 2, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 8, 8] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000681706828 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000681706828 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000681706828/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000681706828/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000681706828 Building ZINC000681706828 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000681706828' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000681706828 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000681706828 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000681706828/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000681706828 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 417) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)Oc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccn1) `ZINC000681706828.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000681706828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000681706828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000681706828 none CC(C)Oc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 20, 30, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 8, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 8, 8] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000681706828 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000681706828/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000681706828 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 418) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)Oc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccn1) `ZINC000681706828.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000681706828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000681706828/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000681706828 none CC(C)Oc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 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, 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] 0 hydrogens 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, 23, 31, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 8, 8, 8, 31, 31, 31, 31, 31, 31, 31, 8, 2, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 8, 8] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000681706828 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000681706828 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000681706828/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000681706828/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000681706828 Building ZINC000758631722 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000758631722' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000758631722 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000758631722 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000758631722/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000758631722 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/419 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(S)[nH]c3c2)cn1) `ZINC000758631722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000758631722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000758631722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000758631722 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(S)[nH]c3c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 14, 8, 6, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 9, 18, 18, 9, 9, 1, 1, 1, 1, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 4, 19, 19, 57, 19, 9] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000758631722 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000758631722/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000758631722 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/420 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/420' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(S)[nH]c3c2)cn1) `ZINC000758631722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000758631722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000758631722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000758631722 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(S)[nH]c3c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 14, 8, 6, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 9, 18, 18, 9, 9, 1, 1, 1, 1, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 4, 17, 17, 51, 17, 9] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000758631722 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000758631722 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000758631722/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000758631722/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000758631722 Building ZINC000758631722 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000758631722' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000758631722 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000758631722 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000758631722/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000758631722 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 419) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(S)[nH]c3c2)cn1) `ZINC000758631722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000758631722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000758631722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000758631722 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(S)[nH]c3c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 14, 8, 6, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 9, 18, 18, 9, 9, 1, 1, 1, 1, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 4, 19, 19, 57, 19, 9] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000758631722 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000758631722/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000758631722 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 420) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(S)[nH]c3c2)cn1) `ZINC000758631722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000758631722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000758631722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000758631722 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(S)[nH]c3c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 14, 8, 6, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 9, 18, 18, 9, 9, 1, 1, 1, 1, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 4, 17, 17, 51, 17, 9] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000758631722 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000758631722 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000758631722/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000758631722/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000758631722 Building ZINC000175357384 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175357384' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175357384 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175357384 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175357384/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175357384 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/421 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C)c(C(=O)N(C)C)c2)cc1) `ZINC000175357384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175357384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175357384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000175357384 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C)c(C(=O)N(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 38, 38, 38, 38, 17, 6, 6, 6, 6, 6, 6, 6, 3, 17, 17, 17, 17, 17, 38, 38, 38, 38, 38, 38, 17, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175357384 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175357384/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175357384 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/422 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/422' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C)c(C(=O)N(C)C)c2)cc1) `ZINC000175357384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175357384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175357384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000175357384 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C)c(C(=O)N(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 18, 18, 18, 18, 18, 18, 37, 37, 37, 37, 18, 6, 6, 6, 6, 6, 6, 6, 3, 18, 18, 18, 18, 18, 37, 37, 37, 37, 37, 37, 18, 6, 6] 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: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175357384 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175357384 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175357384/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175357384/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175357384 Building ZINC000175357384 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175357384' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175357384 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175357384 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175357384/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175357384 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 421) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C)c(C(=O)N(C)C)c2)cc1) `ZINC000175357384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175357384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175357384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000175357384 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C)c(C(=O)N(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 38, 38, 38, 38, 17, 6, 6, 6, 6, 6, 6, 6, 3, 17, 17, 17, 17, 17, 38, 38, 38, 38, 38, 38, 17, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175357384 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175357384/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175357384 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 422) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C)c(C(=O)N(C)C)c2)cc1) `ZINC000175357384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175357384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175357384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000175357384 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C)c(C(=O)N(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 18, 18, 18, 18, 18, 18, 37, 37, 37, 37, 18, 6, 6, 6, 6, 6, 6, 6, 3, 18, 18, 18, 18, 18, 37, 37, 37, 37, 37, 37, 18, 6, 6] 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: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175357384 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175357384 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175357384/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175357384/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175357384 Building ZINC001142654814 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001142654814' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001142654814 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142654814 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001142654814/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001142654814 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/423 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCN1C(=O)OC(C)(C)C) `ZINC001142654814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142654814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001142654814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001142654814 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCN1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 10, 13, 13, 13, 13, 13, 13, 13, 20, 20, 22, 23, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001142654814 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001142654814/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001142654814 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/424 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/424' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCN1C(=O)OC(C)(C)C) `ZINC001142654814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142654814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001142654814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001142654814 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCN1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 13, 13, 13, 13, 13, 13, 13, 21, 21, 22, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001142654814 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC001142654814 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001142654814/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001142654814/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001142654814 Building ZINC001142654814 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001142654814' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001142654814 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142654814 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001142654814/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001142654814 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 423) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCN1C(=O)OC(C)(C)C) `ZINC001142654814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142654814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001142654814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001142654814 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCN1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 10, 13, 13, 13, 13, 13, 13, 13, 20, 20, 22, 23, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001142654814 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001142654814/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001142654814 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 424) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCN1C(=O)OC(C)(C)C) `ZINC001142654814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142654814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001142654814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001142654814 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCN1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 13, 13, 13, 13, 13, 13, 13, 21, 21, 22, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001142654814 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC001142654814 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001142654814/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001142654814/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC001142654814 Building ZINC000175409785 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409785' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409785 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175409785 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409785/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409785 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/425 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/425' -> `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)c2ccc(n3cccn3)cc2)cc1) `ZINC000175409785.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175409785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000175409785 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(n3cccn3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 22, 22, 7, 7, 40, 40, 40, 40, 22, 22, 6, 6, 6, 6, 6, 6, 6, 4, 7, 7, 7, 22, 22, 40, 40, 40, 22, 22, 6, 6] 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: 134 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409785 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409785/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409785 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/426 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/426' -> `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)c2ccc(n3cccn3)cc2)cc1) `ZINC000175409785.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175409785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000175409785 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(n3cccn3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 26, 26, 10, 11, 43, 43, 43, 43, 26, 26, 6, 6, 6, 6, 6, 6, 6, 4, 8, 8, 8, 26, 26, 43, 43, 43, 26, 26, 6, 6] 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: 151 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409785 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175409785 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409785/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409785/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409785 Building ZINC000175409785 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409785' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409785 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175409785 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409785/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409785 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 425) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(n3cccn3)cc2)cc1) `ZINC000175409785.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175409785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000175409785 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(n3cccn3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 22, 22, 7, 7, 40, 40, 40, 40, 22, 22, 6, 6, 6, 6, 6, 6, 6, 4, 7, 7, 7, 22, 22, 40, 40, 40, 22, 22, 6, 6] 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: 134 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409785 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409785/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409785 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 426) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(n3cccn3)cc2)cc1) `ZINC000175409785.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175409785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000175409785 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(n3cccn3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 26, 26, 10, 11, 43, 43, 43, 43, 26, 26, 6, 6, 6, 6, 6, 6, 6, 4, 8, 8, 8, 26, 26, 43, 43, 43, 26, 26, 6, 6] 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: 151 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409785 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175409785 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409785/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409785/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409785 Building ZINC000175409804 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409804' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409804 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175409804 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409804/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409804 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/427 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/427' -> `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)c2ccc(n3cccn3)cc2)cc1) `ZINC000175409804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175409804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000175409804 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(n3cccn3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 26, 26, 8, 8, 43, 43, 43, 43, 26, 26, 6, 6, 6, 6, 6, 6, 6, 4, 8, 8, 8, 26, 26, 43, 43, 43, 26, 26, 6, 6] 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: 152 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409804 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409804/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409804 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/428 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/428' -> `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)c2ccc(n3cccn3)cc2)cc1) `ZINC000175409804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175409804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000175409804 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(n3cccn3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 23, 23, 8, 10, 40, 40, 40, 40, 23, 23, 6, 6, 6, 6, 6, 6, 6, 4, 7, 7, 7, 23, 23, 40, 40, 40, 23, 23, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 138 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409804 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175409804 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409804/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409804/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409804 Building ZINC000175409804 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409804' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409804 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175409804 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409804/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409804 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 427) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(n3cccn3)cc2)cc1) `ZINC000175409804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175409804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000175409804 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(n3cccn3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 26, 26, 8, 8, 43, 43, 43, 43, 26, 26, 6, 6, 6, 6, 6, 6, 6, 4, 8, 8, 8, 26, 26, 43, 43, 43, 26, 26, 6, 6] 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: 152 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409804 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409804/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409804 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 428) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(n3cccn3)cc2)cc1) `ZINC000175409804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175409804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000175409804 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(n3cccn3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 23, 23, 8, 10, 40, 40, 40, 40, 23, 23, 6, 6, 6, 6, 6, 6, 6, 4, 7, 7, 7, 23, 23, 40, 40, 40, 23, 23, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 138 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409804 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175409804 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409804/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409804/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175409804 Building ZINC000159215980 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159215980' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159215980 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000159215980 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159215980/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159215980 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/429 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc2ccc(O)cc2)cc1) `ZINC000159215980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000159215980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159215980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000159215980 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc2ccc(O)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 1, 1, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 6, 6, 1, 1, 1, 1, 3, 3, 7, 7, 20, 20, 20, 35, 43, 43, 37, 43, 43, 43, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 20, 20, 20, 35, 35, 43, 43, 86, 43, 43, 6, 6] 100 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: 296 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159215980 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159215980/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159215980 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/430 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/430' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc2ccc(O)cc2)cc1) `ZINC000159215980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000159215980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159215980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000159215980 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc2ccc(O)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 1, 1, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 8, 8, 20, 20, 20, 37, 44, 44, 37, 44, 44, 44, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 20, 20, 20, 37, 37, 44, 44, 88, 44, 44, 5, 5] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 295 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159215980 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000159215980 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159215980/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159215980/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159215980 Building ZINC000159215980 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159215980' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159215980 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000159215980 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159215980/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159215980 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 429) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc2ccc(O)cc2)cc1) `ZINC000159215980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000159215980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159215980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000159215980 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc2ccc(O)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 1, 1, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 6, 6, 1, 1, 1, 1, 3, 3, 7, 7, 20, 20, 20, 35, 43, 43, 37, 43, 43, 43, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 20, 20, 20, 35, 35, 43, 43, 86, 43, 43, 6, 6] 100 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: 296 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159215980 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159215980/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159215980 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 430) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc2ccc(O)cc2)cc1) `ZINC000159215980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000159215980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159215980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000159215980 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc2ccc(O)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 1, 1, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 8, 8, 20, 20, 20, 37, 44, 44, 37, 44, 44, 44, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 20, 20, 20, 37, 37, 44, 44, 88, 44, 44, 5, 5] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 295 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159215980 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000159215980 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159215980/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159215980/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000159215980 Building ZINC000080983776 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983776' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983776 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000080983776 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983776/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983776 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/431 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@@H]2c2ccccc2)cc1) `ZINC000080983776.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000080983776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000080983776 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 7, 7, 1, 1, 1, 1, 4, 4, 8, 25, 25, 25, 25, 25, 25, 25, 35, 35, 31, 35, 35, 7, 7, 7, 7, 7, 7, 7, 4, 25, 25, 25, 25, 35, 35, 31, 35, 35, 7, 7] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983776 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983776/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983776 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/432 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/432' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@@H]2c2ccccc2)cc1) `ZINC000080983776.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000080983776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983776/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000080983776 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 4, 4, 8, 25, 25, 25, 25, 25, 25, 25, 34, 34, 33, 34, 34, 6, 6, 6, 6, 6, 6, 6, 4, 25, 25, 25, 25, 34, 34, 34, 34, 34, 6, 6] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983776 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000080983776 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983776/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983776/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983776 Building ZINC000080983776 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983776' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983776 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000080983776 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983776/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983776 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 431) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/431: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@@H]2c2ccccc2)cc1) `ZINC000080983776.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000080983776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000080983776 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 7, 7, 1, 1, 1, 1, 4, 4, 8, 25, 25, 25, 25, 25, 25, 25, 35, 35, 31, 35, 35, 7, 7, 7, 7, 7, 7, 7, 4, 25, 25, 25, 25, 35, 35, 31, 35, 35, 7, 7] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983776 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983776/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983776 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 432) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/432: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@@H]2c2ccccc2)cc1) `ZINC000080983776.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000080983776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983776/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000080983776 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 4, 4, 8, 25, 25, 25, 25, 25, 25, 25, 34, 34, 33, 34, 34, 6, 6, 6, 6, 6, 6, 6, 4, 25, 25, 25, 25, 34, 34, 34, 34, 34, 6, 6] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983776 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000080983776 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983776/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983776/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983776 Building ZINC000080983779 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983779' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983779 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000080983779 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983779/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983779 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/433 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@@H]2c2ccccc2)cc1) `ZINC000080983779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000080983779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000080983779 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 4, 4, 8, 25, 25, 25, 25, 25, 25, 25, 34, 34, 25, 34, 34, 6, 6, 6, 6, 6, 6, 6, 4, 25, 25, 25, 25, 34, 34, 25, 34, 34, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983779 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983779/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983779 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/434 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/434' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@@H]2c2ccccc2)cc1) `ZINC000080983779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000080983779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000080983779 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 4, 4, 7, 22, 22, 22, 22, 22, 22, 22, 32, 32, 22, 32, 32, 6, 6, 6, 6, 6, 6, 6, 4, 22, 22, 22, 22, 32, 32, 25, 32, 32, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983779 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000080983779 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983779/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983779/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983779 Building ZINC000080983779 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983779' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983779 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000080983779 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983779/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983779 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 433) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@@H]2c2ccccc2)cc1) `ZINC000080983779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000080983779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000080983779 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 4, 4, 8, 25, 25, 25, 25, 25, 25, 25, 34, 34, 25, 34, 34, 6, 6, 6, 6, 6, 6, 6, 4, 25, 25, 25, 25, 34, 34, 25, 34, 34, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983779 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983779/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983779 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 434) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@@H]2c2ccccc2)cc1) `ZINC000080983779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000080983779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000080983779 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 4, 4, 7, 22, 22, 22, 22, 22, 22, 22, 32, 32, 22, 32, 32, 6, 6, 6, 6, 6, 6, 6, 4, 22, 22, 22, 22, 32, 32, 25, 32, 32, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983779 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000080983779 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983779/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983779/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983779 Building ZINC000080983780 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983780' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983780 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000080983780 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983780/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983780 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/435 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@H]2c2ccccc2)cc1) `ZINC000080983780.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000080983780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000080983780 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 4, 4, 7, 22, 22, 22, 22, 22, 22, 22, 32, 32, 22, 32, 32, 6, 6, 6, 6, 6, 6, 6, 4, 22, 22, 22, 22, 32, 32, 22, 32, 32, 6, 6] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983780 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983780/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983780 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/436 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/436' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@H]2c2ccccc2)cc1) `ZINC000080983780.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000080983780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983780/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000080983780 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 4, 4, 8, 26, 26, 26, 26, 26, 26, 26, 35, 35, 26, 35, 35, 6, 6, 6, 6, 6, 6, 6, 4, 26, 26, 26, 26, 35, 35, 26, 35, 35, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983780 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000080983780 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983780/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983780/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983780 Building ZINC000080983780 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983780' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983780 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000080983780 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983780/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983780 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 435) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@H]2c2ccccc2)cc1) `ZINC000080983780.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000080983780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000080983780 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 4, 4, 7, 22, 22, 22, 22, 22, 22, 22, 32, 32, 22, 32, 32, 6, 6, 6, 6, 6, 6, 6, 4, 22, 22, 22, 22, 32, 32, 22, 32, 32, 6, 6] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983780 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983780/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983780 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 436) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@H]2c2ccccc2)cc1) `ZINC000080983780.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000080983780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983780/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000080983780 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 4, 4, 8, 26, 26, 26, 26, 26, 26, 26, 35, 35, 26, 35, 35, 6, 6, 6, 6, 6, 6, 6, 4, 26, 26, 26, 26, 35, 35, 26, 35, 35, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983780 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000080983780 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983780/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983780/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983780 Building ZINC000080983784 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983784' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983784 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000080983784 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983784/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983784 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/437 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@H]2c2ccccc2)cc1) `ZINC000080983784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000080983784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000080983784 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 4, 4, 8, 25, 25, 25, 25, 25, 25, 25, 34, 34, 25, 34, 34, 6, 6, 6, 6, 6, 6, 6, 4, 25, 25, 25, 25, 34, 34, 25, 34, 34, 6, 6] 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]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983784 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983784/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983784 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/438 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/438' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@H]2c2ccccc2)cc1) `ZINC000080983784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000080983784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000080983784 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 1, 8, 8, 1, 1, 1, 1, 5, 5, 9, 26, 26, 26, 26, 26, 26, 26, 35, 35, 26, 35, 35, 8, 8, 8, 8, 8, 8, 8, 5, 26, 26, 26, 26, 35, 35, 26, 35, 35, 8, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983784 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000080983784 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983784/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983784/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983784 Building ZINC000080983784 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983784' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983784 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000080983784 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983784/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983784 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 437) grep: /scratch/xiaobo/83235/xao-8058115.15/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([C@@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@H]2c2ccccc2)cc1) `ZINC000080983784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000080983784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000080983784 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 6, 6, 1, 1, 1, 1, 4, 4, 8, 25, 25, 25, 25, 25, 25, 25, 34, 34, 25, 34, 34, 6, 6, 6, 6, 6, 6, 6, 4, 25, 25, 25, 25, 34, 34, 25, 34, 34, 6, 6] 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]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983784 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983784/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983784 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 438) grep: /scratch/xiaobo/83235/xao-8058115.15/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([C@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@H]2c2ccccc2)cc1) `ZINC000080983784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000080983784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000080983784 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 1, 8, 8, 1, 1, 1, 1, 5, 5, 9, 26, 26, 26, 26, 26, 26, 26, 35, 35, 26, 35, 35, 8, 8, 8, 8, 8, 8, 8, 5, 26, 26, 26, 26, 35, 35, 26, 35, 35, 8, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983784 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000080983784 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983784/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983784/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000080983784 Building ZINC000431233961 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233961' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233961 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000431233961 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233961/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233961 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/439 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@]2(CCO[C@H](C)C2)C1) `ZINC000431233961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000431233961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000431233961 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@]2(CCO[C@H](C)C2)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 22, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 44, 44, 44, 44, 44, 44, 44, 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: 73 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233961 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233961/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233961 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/440 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/440' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@]2(CCO[C@H](C)C2)C1) `ZINC000431233961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000431233961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000431233961 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@]2(CCO[C@H](C)C2)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 13, 26, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 3, 3, 3, 3, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 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, 47, 48]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233961 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000431233961 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233961/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233961/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233961 Building ZINC000431233961 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233961' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233961 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000431233961 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233961/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233961 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 439) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@]2(CCO[C@H](C)C2)C1) `ZINC000431233961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000431233961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000431233961 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@]2(CCO[C@H](C)C2)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 22, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 44, 44, 44, 44, 44, 44, 44, 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: 73 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233961 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233961/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233961 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 440) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@]2(CCO[C@H](C)C2)C1) `ZINC000431233961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000431233961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000431233961 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@]2(CCO[C@H](C)C2)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 13, 26, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 3, 3, 3, 3, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 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, 47, 48]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233961 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000431233961 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233961/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233961/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233961 Building ZINC000431233963 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233963' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233963 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000431233963 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233963/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233963 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/441 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@]2(CCO[C@@H](C)C2)C1) `ZINC000431233963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000431233963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000431233963 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@]2(CCO[C@@H](C)C2)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 19, 24, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 4, 4, 4, 4, 4, 4, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233963 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233963/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233963 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/442 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/442' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@]2(CCO[C@@H](C)C2)C1) `ZINC000431233963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000431233963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000431233963 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@]2(CCO[C@@H](C)C2)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 16, 21, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4, 4, 4, 4, 4, 4, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42] 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233963 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000431233963 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233963/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233963/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233963 Building ZINC000431233963 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233963' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233963 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000431233963 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233963/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233963 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 441) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@]2(CCO[C@@H](C)C2)C1) `ZINC000431233963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000431233963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000431233963 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@]2(CCO[C@@H](C)C2)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 19, 24, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 4, 4, 4, 4, 4, 4, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233963 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233963/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233963 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 442) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@]2(CCO[C@@H](C)C2)C1) `ZINC000431233963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000431233963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000431233963 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@]2(CCO[C@@H](C)C2)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 16, 21, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4, 4, 4, 4, 4, 4, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42] 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233963 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000431233963 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233963/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233963/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233963 Building ZINC000431233965 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233965' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233965 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000431233965 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233965/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233965 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/443 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@]2(CCO[C@@H](C)C2)C1) `ZINC000431233965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000431233965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000431233965 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@]2(CCO[C@@H](C)C2)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 15, 22, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 4, 4, 4, 4, 4, 4, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 47 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 74 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233965 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233965/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233965 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/444 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/444' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@]2(CCO[C@@H](C)C2)C1) `ZINC000431233965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000431233965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000431233965 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@]2(CCO[C@@H](C)C2)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 14, 28, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 4, 4, 4, 4, 4, 4, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233965 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000431233965 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233965/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233965/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233965 Building ZINC000431233965 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233965' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233965 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000431233965 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233965/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233965 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 443) grep: /scratch/xiaobo/83235/xao-8058115.15/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(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@]2(CCO[C@@H](C)C2)C1) `ZINC000431233965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000431233965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000431233965 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@]2(CCO[C@@H](C)C2)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 15, 22, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 4, 4, 4, 4, 4, 4, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 47 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 74 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233965 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233965/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233965 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 444) grep: /scratch/xiaobo/83235/xao-8058115.15/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(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@]2(CCO[C@@H](C)C2)C1) `ZINC000431233965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000431233965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000431233965 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@]2(CCO[C@@H](C)C2)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 14, 28, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 4, 4, 4, 4, 4, 4, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233965 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000431233965 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233965/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233965/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233965 Building ZINC000431233967 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233967' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233967 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000431233967 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233967/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233967 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/445 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@]2(CCO[C@H](C)C2)C1) `ZINC000431233967.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000431233967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000431233967 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@]2(CCO[C@H](C)C2)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 14, 21, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233967 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233967/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233967 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/446 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/446' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@]2(CCO[C@H](C)C2)C1) `ZINC000431233967.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000431233967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233967/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000431233967 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@]2(CCO[C@H](C)C2)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 12, 22, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 4, 4, 4, 4, 4, 4, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233967 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000431233967 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233967/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233967/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233967 Building ZINC000431233967 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233967' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233967 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000431233967 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233967/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233967 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 445) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@]2(CCO[C@H](C)C2)C1) `ZINC000431233967.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000431233967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000431233967 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@]2(CCO[C@H](C)C2)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 14, 21, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233967 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233967/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233967 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 446) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@]2(CCO[C@H](C)C2)C1) `ZINC000431233967.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000431233967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233967/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000431233967 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@]2(CCO[C@H](C)C2)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 12, 22, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 4, 4, 4, 4, 4, 4, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233967 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000431233967 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233967/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233967/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431233967 Building ZINC000138880175 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000138880175' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000138880175 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000138880175 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000138880175/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000138880175 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/447 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(F)cc(C(N)=O)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000138880175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000138880175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000138880175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000138880175 none Cc1c(F)cc(C(N)=O)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 8, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 23, 23, 16, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 16, 16, 16, 16, 23, 23, 16, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000138880175 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000138880175/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000138880175 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/448 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/448' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(F)cc(C(N)=O)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000138880175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000138880175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000138880175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000138880175 none Cc1c(F)cc(C(N)=O)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 8, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 23, 23, 16, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 16, 16, 16, 16, 23, 23, 16, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000138880175 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000138880175 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000138880175/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000138880175/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000138880175 Building ZINC000138880175 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000138880175' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000138880175 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000138880175 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000138880175/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000138880175 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 447) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1c(F)cc(C(N)=O)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000138880175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000138880175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000138880175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000138880175 none Cc1c(F)cc(C(N)=O)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 8, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 23, 23, 16, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 16, 16, 16, 16, 23, 23, 16, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000138880175 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000138880175/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000138880175 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 448) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1c(F)cc(C(N)=O)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000138880175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000138880175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000138880175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000138880175 none Cc1c(F)cc(C(N)=O)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 8, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 23, 23, 16, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 16, 16, 16, 16, 23, 23, 16, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000138880175 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000138880175 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000138880175/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000138880175/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000138880175 Building ZINC000081650508 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000081650508' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000081650508 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000081650508 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000081650508/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000081650508 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/449 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2ccc(N(C)C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)cc2s1) `ZINC000081650508.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000081650508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000081650508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000081650508 none Cc1nc2ccc(N(C)C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 6, 4, 6, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27] 46 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 48 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000081650508 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000081650508/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000081650508 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/450 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/450' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2ccc(N(C)C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)cc2s1) `ZINC000081650508.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000081650508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000081650508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000081650508 none Cc1nc2ccc(N(C)C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 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] 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: [25, 25, 25, 25, 25, 25, 6, 4, 6, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25] 46 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 46 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000081650508 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000081650508 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000081650508/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000081650508/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000081650508 Building ZINC000081650508 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000081650508' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000081650508 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000081650508 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000081650508/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000081650508 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 449) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nc2ccc(N(C)C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)cc2s1) `ZINC000081650508.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000081650508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000081650508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000081650508 none Cc1nc2ccc(N(C)C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 6, 4, 6, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27] 46 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 48 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000081650508 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000081650508/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000081650508 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 450) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nc2ccc(N(C)C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)cc2s1) `ZINC000081650508.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000081650508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000081650508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000081650508 none Cc1nc2ccc(N(C)C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 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] 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: [25, 25, 25, 25, 25, 25, 6, 4, 6, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25] 46 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 46 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000081650508 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000081650508 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000081650508/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000081650508/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000081650508 Building ZINC000431269003 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431269003' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431269003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000431269003 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431269003/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431269003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/451 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2c3c(ccc2Cl)CC(C)(C)O3)cn1) `ZINC000431269003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000431269003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431269003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000431269003 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2c3c(ccc2Cl)CC(C)(C)O3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 5, 5, 5, 21, 30, 30, 30, 21, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 10, 10, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431269003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431269003/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431269003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/452 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/452' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2c3c(ccc2Cl)CC(C)(C)O3)cn1) `ZINC000431269003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000431269003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431269003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000431269003 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2c3c(ccc2Cl)CC(C)(C)O3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 6, 6, 6, 21, 28, 28, 28, 21, 28, 28, 28, 28, 28, 28, 10, 10, 10, 10, 10, 10, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431269003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000431269003 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431269003/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431269003/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431269003 Building ZINC000431269003 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431269003' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431269003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000431269003 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431269003/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431269003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 451) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2c3c(ccc2Cl)CC(C)(C)O3)cn1) `ZINC000431269003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000431269003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431269003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000431269003 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2c3c(ccc2Cl)CC(C)(C)O3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 5, 5, 5, 21, 30, 30, 30, 21, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 10, 10, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431269003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431269003/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431269003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 452) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2c3c(ccc2Cl)CC(C)(C)O3)cn1) `ZINC000431269003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000431269003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431269003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000431269003 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2c3c(ccc2Cl)CC(C)(C)O3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 6, 6, 6, 21, 28, 28, 28, 21, 28, 28, 28, 28, 28, 28, 10, 10, 10, 10, 10, 10, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431269003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000431269003 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431269003/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431269003/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431269003 Building ZINC000083011947 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000083011947' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000083011947 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000083011947 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000083011947/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000083011947 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/453 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)Cc2nc3c(s2)CCCC3)cc1) `ZINC000083011947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000083011947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000083011947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000083011947 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)Cc2nc3c(s2)CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 1, 14, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 2, 2, 5, 5, 18, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 18, 18, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000083011947 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000083011947/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000083011947 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/454 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/454' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2nc3c(s2)CCCC3)cc1) `ZINC000083011947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000083011947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000083011947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000083011947 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2nc3c(s2)CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 1, 14, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 2, 2, 5, 5, 18, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 18, 18, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000083011947 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000083011947 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000083011947/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000083011947/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000083011947 Building ZINC000083011947 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000083011947' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000083011947 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000083011947 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000083011947/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000083011947 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 453) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)Cc2nc3c(s2)CCCC3)cc1) `ZINC000083011947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000083011947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000083011947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000083011947 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)Cc2nc3c(s2)CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 1, 14, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 2, 2, 5, 5, 18, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 18, 18, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000083011947 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000083011947/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000083011947 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 454) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2nc3c(s2)CCCC3)cc1) `ZINC000083011947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000083011947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000083011947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000083011947 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2nc3c(s2)CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 1, 14, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 2, 2, 5, 5, 18, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 18, 18, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000083011947 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000083011947 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000083011947/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000083011947/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000083011947 Building ZINC000084070450 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084070450' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084070450 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000084070450 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084070450/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084070450 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/455 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(CCN(C)C)Cc2cccs2)cc1) `ZINC000084070450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000084070450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084070450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000084070450 none COc1ccc([C@]([O-])([SiH3])C(=O)N(CCN(C)C)Cc2cccs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 14, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 3, 10, 11, 18, 18, 3, 9, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 10, 10, 11, 11, 18, 18, 18, 18, 18, 18, 9, 9, 15, 15, 15, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084070450 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084070450/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084070450 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/456 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/456' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(CCN(C)C)Cc2cccs2)cc1) `ZINC000084070450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000084070450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084070450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000084070450 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(CCN(C)C)Cc2cccs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 14, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 3, 10, 10, 18, 18, 3, 9, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18, 9, 9, 15, 15, 15, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084070450 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000084070450 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084070450/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084070450/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084070450 Building ZINC000084070450 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084070450' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084070450 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000084070450 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084070450/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084070450 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 455) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)N(CCN(C)C)Cc2cccs2)cc1) `ZINC000084070450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000084070450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084070450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000084070450 none COc1ccc([C@]([O-])([SiH3])C(=O)N(CCN(C)C)Cc2cccs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 14, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 3, 10, 11, 18, 18, 3, 9, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 10, 10, 11, 11, 18, 18, 18, 18, 18, 18, 9, 9, 15, 15, 15, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084070450 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084070450/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084070450 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 456) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N(CCN(C)C)Cc2cccs2)cc1) `ZINC000084070450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000084070450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084070450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000084070450 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(CCN(C)C)Cc2cccs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 14, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 3, 10, 10, 18, 18, 3, 9, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18, 9, 9, 15, 15, 15, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084070450 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000084070450 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084070450/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084070450/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084070450 Building ZINC000431561178 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431561178' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431561178 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000431561178 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431561178/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431561178 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/457 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CCO)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000431561178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000431561178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431561178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000431561178 none COc1cc(CCO)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 7, 7, 5, 7, 14, 18, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 7, 14, 14, 18, 18, 54, 7, 7, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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/83235/xao-8058115.15/working/building/ZINC000431561178 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431561178/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431561178 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/458 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/458' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CCO)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000431561178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000431561178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431561178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000431561178 none COc1cc(CCO)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 7, 7, 6, 7, 14, 18, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 7, 14, 14, 18, 18, 54, 7, 7, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431561178 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000431561178 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431561178/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431561178/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431561178 Building ZINC000431561178 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431561178' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431561178 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000431561178 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431561178/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431561178 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 457) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1cc(CCO)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000431561178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000431561178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431561178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000431561178 none COc1cc(CCO)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 7, 7, 5, 7, 14, 18, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 7, 14, 14, 18, 18, 54, 7, 7, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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/83235/xao-8058115.15/working/building/ZINC000431561178 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431561178/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431561178 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 458) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1cc(CCO)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000431561178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000431561178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431561178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000431561178 none COc1cc(CCO)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 7, 7, 6, 7, 14, 18, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 7, 14, 14, 18, 18, 54, 7, 7, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431561178 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000431561178 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431561178/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431561178/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431561178 Building ZINC000084560769 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560769' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560769 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000084560769 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560769/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560769 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/459 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)Oc1cccc(F)c1) `ZINC000084560769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000084560769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000084560769 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)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', 'O.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 15, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 15, 27, 47, 47, 47, 47, 47, 47, 19, 19, 19, 19, 19, 10, 10, 2, 2, 2, 4, 4, 4, 2, 2, 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, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560769 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560769/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560769 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/460 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/460' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)Oc1cccc(F)c1) `ZINC000084560769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000084560769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000084560769 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(OC)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', 'O.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 9, 13, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 13, 25, 45, 45, 45, 45, 45, 45, 16, 16, 16, 16, 16, 9, 9, 2, 2, 2, 4, 4, 4, 2, 2, 45, 45, 45, 45] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 130 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560769 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000084560769 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560769/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560769/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560769 Building ZINC000084560769 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560769' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560769 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000084560769 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560769/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560769 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 459) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)Oc1cccc(F)c1) `ZINC000084560769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000084560769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000084560769 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)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', 'O.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 15, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 15, 27, 47, 47, 47, 47, 47, 47, 19, 19, 19, 19, 19, 10, 10, 2, 2, 2, 4, 4, 4, 2, 2, 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, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560769 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560769/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560769 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 460) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)Oc1cccc(F)c1) `ZINC000084560769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000084560769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000084560769 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(OC)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', 'O.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 9, 13, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 13, 25, 45, 45, 45, 45, 45, 45, 16, 16, 16, 16, 16, 9, 9, 2, 2, 2, 4, 4, 4, 2, 2, 45, 45, 45, 45] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 130 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560769 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000084560769 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560769/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560769/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560769 Building ZINC000084560770 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560770' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560770 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000084560770 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560770/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560770 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/461 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)Oc1cccc(F)c1) `ZINC000084560770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000084560770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000084560770 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)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', 'O.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 9, 13, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 13, 25, 45, 45, 45, 45, 45, 45, 16, 16, 16, 16, 16, 9, 9, 2, 2, 2, 4, 4, 4, 2, 2, 45, 45, 45, 45] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 130 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560770 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560770/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560770 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/462 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/462' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)Oc1cccc(F)c1) `ZINC000084560770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000084560770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000084560770 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(OC)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', 'O.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 13, 10, 15, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 15, 26, 47, 47, 47, 47, 47, 47, 18, 18, 18, 18, 18, 10, 10, 2, 2, 2, 4, 4, 4, 2, 2, 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, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 156 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560770 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000084560770 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560770/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560770/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560770 Building ZINC000084560770 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560770' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560770 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000084560770 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560770/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560770 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 461) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)Oc1cccc(F)c1) `ZINC000084560770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000084560770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000084560770 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)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', 'O.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 9, 13, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 13, 25, 45, 45, 45, 45, 45, 45, 16, 16, 16, 16, 16, 9, 9, 2, 2, 2, 4, 4, 4, 2, 2, 45, 45, 45, 45] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 130 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560770 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560770/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560770 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 462) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)Oc1cccc(F)c1) `ZINC000084560770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000084560770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000084560770 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(OC)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', 'O.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 13, 10, 15, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 15, 26, 47, 47, 47, 47, 47, 47, 18, 18, 18, 18, 18, 10, 10, 2, 2, 2, 4, 4, 4, 2, 2, 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, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 156 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560770 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000084560770 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560770/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560770/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000084560770 Building ZINC000529600981 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600981' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529600981 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600981/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/463 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@H]1CCCOC1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529600981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529600981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000529600981 none O=C(NCC[C@H]1CCCOC1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 39, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 15, 15, 27, 27, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600981/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/464 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/464' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@H]1CCCOC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529600981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529600981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000529600981 none O=C(NCC[C@H]1CCCOC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 13, 39, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 1, 1, 3, 3, 2, 13, 13, 25, 25, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529600981 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600981/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600981/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600981 Building ZINC000529600981 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600981' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529600981 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600981/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 463) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NCC[C@H]1CCCOC1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529600981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529600981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000529600981 none O=C(NCC[C@H]1CCCOC1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 39, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 15, 15, 27, 27, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600981/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 464) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NCC[C@H]1CCCOC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529600981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529600981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000529600981 none O=C(NCC[C@H]1CCCOC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 13, 39, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 1, 1, 3, 3, 2, 13, 13, 25, 25, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529600981 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600981/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600981/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600981 Building ZINC000529600982 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600982' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600982 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529600982 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600982/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600982 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/465 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@@H]1CCCOC1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529600982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529600982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000529600982 none O=C(NCC[C@@H]1CCCOC1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 19, 37, 48, 48, 48, 48, 48, 48, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 19, 19, 34, 34, 48, 48, 48, 48, 48, 48, 48, 48, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 192 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600982 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600982/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600982 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/466 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/466' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@@H]1CCCOC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529600982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529600982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000529600982 none O=C(NCC[C@@H]1CCCOC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 18, 35, 48, 48, 48, 48, 48, 48, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 18, 18, 32, 32, 48, 48, 48, 48, 48, 48, 48, 48, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 191 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600982 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529600982 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600982/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600982/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600982 Building ZINC000529600982 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600982' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600982 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529600982 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600982/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600982 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 465) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NCC[C@@H]1CCCOC1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529600982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529600982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000529600982 none O=C(NCC[C@@H]1CCCOC1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 19, 37, 48, 48, 48, 48, 48, 48, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 19, 19, 34, 34, 48, 48, 48, 48, 48, 48, 48, 48, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 192 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600982 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600982/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600982 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 466) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NCC[C@@H]1CCCOC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529600982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529600982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000529600982 none O=C(NCC[C@@H]1CCCOC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 18, 35, 48, 48, 48, 48, 48, 48, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 18, 18, 32, 32, 48, 48, 48, 48, 48, 48, 48, 48, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 191 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600982 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529600982 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600982/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600982/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529600982 Building ZINC000431707740 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431707740' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431707740 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000431707740 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431707740/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431707740 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/467 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2C[C@H]2c2ccc(Cl)cc2Cl)cn1) `ZINC000431707740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000431707740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431707740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000431707740 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2C[C@H]2c2ccc(Cl)cc2Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 16, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 17, 17, 17, 17, 17, 33, 33, 20, 27, 33, 33, 33, 8, 8, 8, 8, 8, 8, 4, 17, 17, 33, 33, 33, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431707740 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431707740/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431707740 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/468 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/468' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2C[C@H]2c2ccc(Cl)cc2Cl)cn1) `ZINC000431707740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000431707740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431707740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000431707740 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2C[C@H]2c2ccc(Cl)cc2Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 16, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 34, 34, 16, 27, 34, 34, 34, 10, 10, 10, 10, 10, 10, 5, 15, 15, 34, 34, 34, 10] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431707740 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000431707740 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431707740/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431707740/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431707740 Building ZINC000431707740 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431707740' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431707740 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000431707740 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431707740/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431707740 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 467) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2C[C@H]2c2ccc(Cl)cc2Cl)cn1) `ZINC000431707740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000431707740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431707740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000431707740 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2C[C@H]2c2ccc(Cl)cc2Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 16, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 17, 17, 17, 17, 17, 33, 33, 20, 27, 33, 33, 33, 8, 8, 8, 8, 8, 8, 4, 17, 17, 33, 33, 33, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431707740 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431707740/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431707740 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 468) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2C[C@H]2c2ccc(Cl)cc2Cl)cn1) `ZINC000431707740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000431707740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431707740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000431707740 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2C[C@H]2c2ccc(Cl)cc2Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 16, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 34, 34, 16, 27, 34, 34, 34, 10, 10, 10, 10, 10, 10, 5, 15, 15, 34, 34, 34, 10] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431707740 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000431707740 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431707740/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431707740/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000431707740 Building ZINC000529619957 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619957' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619957 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529619957 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619957/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619957 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/469 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(C)COc3ccccc3O2)cc1) `ZINC000529619957.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529619957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000529619957 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(C)COc3ccccc3O2)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 50, 50, 50, 50, 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]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619957 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619957/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619957 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/470 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/470' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@]2(C)COc3ccccc3O2)cc1) `ZINC000529619957.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529619957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619957/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000529619957 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@]2(C)COc3ccccc3O2)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 50, 50, 50, 50, 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]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619957 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529619957 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619957/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619957/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619957 Building ZINC000529619957 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619957' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619957 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529619957 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619957/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619957 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 469) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(C)COc3ccccc3O2)cc1) `ZINC000529619957.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529619957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000529619957 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(C)COc3ccccc3O2)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 50, 50, 50, 50, 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]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619957 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619957/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619957 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 470) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@]2(C)COc3ccccc3O2)cc1) `ZINC000529619957.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529619957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619957/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000529619957 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@]2(C)COc3ccccc3O2)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 50, 50, 50, 50, 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]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619957 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529619957 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619957/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619957/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619957 Building ZINC000529619965 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619965' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619965 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529619965 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619965/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619965 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/471 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(C)COc3ccccc3O2)cc1) `ZINC000529619965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529619965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000529619965 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(C)COc3ccccc3O2)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 50, 50, 50, 50, 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619965 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619965/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619965 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/472 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/472' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(C)COc3ccccc3O2)cc1) `ZINC000529619965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529619965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000529619965 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(C)COc3ccccc3O2)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 50, 50, 50, 50, 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619965 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529619965 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619965/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619965/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619965 Building ZINC000529619965 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619965' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619965 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529619965 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619965/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619965 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 471) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(C)COc3ccccc3O2)cc1) `ZINC000529619965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529619965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000529619965 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(C)COc3ccccc3O2)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 50, 50, 50, 50, 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619965 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619965/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619965 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 472) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(C)COc3ccccc3O2)cc1) `ZINC000529619965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529619965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000529619965 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(C)COc3ccccc3O2)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 50, 50, 50, 50, 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619965 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529619965 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619965/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619965/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529619965 Building ZINC000529613549 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529613549' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529613549 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529613549 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529613549/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529613549 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/473 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/473' -> `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)NCC1CCc2ccccc2CC1) `ZINC000529613549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529613549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529613549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000529613549 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1CCc2ccccc2CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 25, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 44, 44, 44, 44, 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, 49]) total number of confs: 133 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529613549 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529613549/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529613549 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/474 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/474' -> `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)NCC1CCc2ccccc2CC1) `ZINC000529613549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529613549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529613549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000529613549 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1CCc2ccccc2CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 21, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 15, 15, 43, 43, 43, 43, 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, 49]) total number of confs: 128 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529613549 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529613549 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529613549/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529613549/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529613549 Building ZINC000529613549 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529613549' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529613549 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529613549 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529613549/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529613549 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 473) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1CCc2ccccc2CC1) `ZINC000529613549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529613549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529613549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000529613549 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1CCc2ccccc2CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 25, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 44, 44, 44, 44, 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, 49]) total number of confs: 133 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529613549 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529613549/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529613549 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 474) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1CCc2ccccc2CC1) `ZINC000529613549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529613549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529613549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000529613549 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1CCc2ccccc2CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 21, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 15, 15, 43, 43, 43, 43, 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, 49]) total number of confs: 128 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529613549 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529613549 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529613549/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529613549/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529613549 Building ZINC000760602246 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602246' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602246 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760602246 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602246/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602246 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/475 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)c1nc2ccccc2o1) `ZINC000760602246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760602246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000760602246 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)c1nc2ccccc2o1 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 16, 16, 16, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602246 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602246/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602246 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/476 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/476' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)c1nc2ccccc2o1) `ZINC000760602246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760602246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000760602246 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)c1nc2ccccc2o1 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 14, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 24, 24, 24, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602246 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000760602246 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602246/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602246/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602246 Building ZINC000760602246 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602246' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602246 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760602246 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602246/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602246 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 475) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)c1nc2ccccc2o1) `ZINC000760602246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760602246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000760602246 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)c1nc2ccccc2o1 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 16, 16, 16, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602246 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602246/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602246 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 476) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)c1nc2ccccc2o1) `ZINC000760602246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760602246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000760602246 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)c1nc2ccccc2o1 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 14, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 24, 24, 24, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602246 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000760602246 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602246/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602246/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602246 Building ZINC000760602247 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602247' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602247 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760602247 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602247/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602247 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/477 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H](C)c1nc2ccccc2o1) `ZINC000760602247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760602247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000760602247 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H](C)c1nc2ccccc2o1 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 14, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 25, 25, 25, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602247 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602247/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602247 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/478 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/478' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)c1nc2ccccc2o1) `ZINC000760602247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760602247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000760602247 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)c1nc2ccccc2o1 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 16, 16, 16, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602247 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000760602247 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602247/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602247/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602247 Building ZINC000760602247 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602247' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602247 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760602247 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602247/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602247 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 477) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H](C)c1nc2ccccc2o1) `ZINC000760602247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760602247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000760602247 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H](C)c1nc2ccccc2o1 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 14, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 25, 25, 25, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602247 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602247/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602247 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 478) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)c1nc2ccccc2o1) `ZINC000760602247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760602247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000760602247 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)c1nc2ccccc2o1 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 16, 16, 16, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602247 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000760602247 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602247/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602247/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760602247 Building ZINC000529677003 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529677003' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529677003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529677003 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529677003/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529677003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/479 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1ncc2c(n1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C2) `ZINC000529677003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529677003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529677003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000529677003 none CC(C)(C)c1ncc2c(n1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 5, 1, 8, 1, 1, 1, 8, 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, 7, 7, 3, 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, 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, 32, 44, 44, 32, 32, 32, 32, 32, 32, 32, 32, 11, 2, 17, 1, 1, 1, 6, 6, 1, 1, 6, 6, 32, 44, 44, 44, 44, 44, 44, 44, 44, 44, 32, 32, 32, 32, 32, 6, 6, 6, 6, 32, 32] 47 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: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529677003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529677003/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529677003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/480 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/480' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1ncc2c(n1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C2) `ZINC000529677003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529677003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529677003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000529677003 none CC(C)(C)c1ncc2c(n1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 5, 1, 8, 1, 1, 1, 8, 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, 7, 7, 3, 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, 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: [46, 32, 46, 46, 32, 32, 32, 32, 32, 32, 32, 32, 11, 2, 17, 1, 1, 1, 6, 6, 1, 1, 6, 6, 32, 46, 46, 46, 46, 46, 46, 46, 46, 46, 32, 32, 32, 32, 32, 6, 6, 6, 6, 32, 32] 49 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529677003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529677003 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529677003/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529677003/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529677003 Building ZINC000529677003 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529677003' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529677003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529677003 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529677003/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529677003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 479) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)c1ncc2c(n1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C2) `ZINC000529677003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529677003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529677003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000529677003 none CC(C)(C)c1ncc2c(n1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 5, 1, 8, 1, 1, 1, 8, 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, 7, 7, 3, 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, 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, 32, 44, 44, 32, 32, 32, 32, 32, 32, 32, 32, 11, 2, 17, 1, 1, 1, 6, 6, 1, 1, 6, 6, 32, 44, 44, 44, 44, 44, 44, 44, 44, 44, 32, 32, 32, 32, 32, 6, 6, 6, 6, 32, 32] 47 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: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529677003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529677003/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529677003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 480) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)c1ncc2c(n1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C2) `ZINC000529677003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529677003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529677003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000529677003 none CC(C)(C)c1ncc2c(n1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 5, 1, 8, 1, 1, 1, 8, 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, 7, 7, 3, 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, 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: [46, 32, 46, 46, 32, 32, 32, 32, 32, 32, 32, 32, 11, 2, 17, 1, 1, 1, 6, 6, 1, 1, 6, 6, 32, 46, 46, 46, 46, 46, 46, 46, 46, 46, 32, 32, 32, 32, 32, 6, 6, 6, 6, 32, 32] 49 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529677003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529677003 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529677003/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529677003/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529677003 Building ZINC000529695001 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529695001' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529695001 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529695001 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529695001/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529695001 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/481 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC(C)(C)c2nc3ccccc3s2)cn1) `ZINC000529695001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529695001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529695001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000529695001 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC(C)(C)c2nc3ccccc3s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 13, 13, 13, 13, 13, 6, 4, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/83235/xao-8058115.15/working/building/ZINC000529695001 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529695001/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529695001 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/482 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/482' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC(C)(C)c2nc3ccccc3s2)cn1) `ZINC000529695001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529695001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529695001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000529695001 none CCn1cc([C@]([O-])([SiH3])C(=O)NC(C)(C)c2nc3ccccc3s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 13, 13, 13, 13, 13, 6, 4, 8, 8, 8, 8, 8, 8, 21, 21, 21, 21, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529695001 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529695001 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529695001/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529695001/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529695001 Building ZINC000529695001 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529695001' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529695001 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529695001 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529695001/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529695001 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 481) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NC(C)(C)c2nc3ccccc3s2)cn1) `ZINC000529695001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529695001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529695001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000529695001 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC(C)(C)c2nc3ccccc3s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 13, 13, 13, 13, 13, 6, 4, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/83235/xao-8058115.15/working/building/ZINC000529695001 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529695001/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529695001 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 482) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCn1cc([C@]([O-])([SiH3])C(=O)NC(C)(C)c2nc3ccccc3s2)cn1) `ZINC000529695001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529695001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529695001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000529695001 none CCn1cc([C@]([O-])([SiH3])C(=O)NC(C)(C)c2nc3ccccc3s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 13, 13, 13, 13, 13, 6, 4, 8, 8, 8, 8, 8, 8, 21, 21, 21, 21, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529695001 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529695001 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529695001/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529695001/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529695001 Building ZINC000529684672 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684672' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684672 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529684672 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684672/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684672 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/483 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2Cc3cc(Cl)ccc3[C@@H]21) `ZINC000529684672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529684672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529684672 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2Cc3cc(Cl)ccc3[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 1, 1, 1, 16, 1, 1, 1, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 9, 9, 1, 9, 9, 1, 1, 1, 1, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 11, 11, 11, 9, 9, 9, 9, 11, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 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: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684672 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684672/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684672 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/484 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/484' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2Cc3cc(Cl)ccc3[C@@H]21) `ZINC000529684672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529684672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529684672 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2Cc3cc(Cl)ccc3[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 1, 1, 1, 16, 1, 1, 1, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 9, 9, 4, 9, 9, 1, 1, 1, 1, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 11, 11, 11, 9, 9, 9, 9, 10, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684672 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529684672 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684672/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684672/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684672 Building ZINC000529684672 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684672' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684672 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529684672 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684672/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684672 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 483) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2Cc3cc(Cl)ccc3[C@@H]21) `ZINC000529684672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529684672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529684672 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2Cc3cc(Cl)ccc3[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 1, 1, 1, 16, 1, 1, 1, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 9, 9, 1, 9, 9, 1, 1, 1, 1, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 11, 11, 11, 9, 9, 9, 9, 11, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 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: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684672 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684672/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684672 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 484) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2Cc3cc(Cl)ccc3[C@@H]21) `ZINC000529684672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529684672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529684672 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2Cc3cc(Cl)ccc3[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 1, 1, 1, 16, 1, 1, 1, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 9, 9, 4, 9, 9, 1, 1, 1, 1, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 11, 11, 11, 9, 9, 9, 9, 10, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684672 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529684672 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684672/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684672/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684672 Building ZINC000529684673 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684673' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684673 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529684673 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684673/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684673 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/485 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2Cc3cc(Cl)ccc3[C@@H]12) `ZINC000529684673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529684673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529684673 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2Cc3cc(Cl)ccc3[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 1, 1, 1, 16, 1, 1, 1, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 9, 9, 1, 9, 9, 1, 1, 1, 1, 9, 9, 9, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 13, 13, 13, 9, 9, 9, 9, 9, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 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: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684673 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684673/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684673 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/486 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/486' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2Cc3cc(Cl)ccc3[C@@H]12) `ZINC000529684673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529684673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529684673 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2Cc3cc(Cl)ccc3[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 1, 1, 1, 16, 1, 1, 1, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 1, 9, 9, 1, 1, 1, 1, 10, 10, 10, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 15, 9, 9, 9, 9, 10, 33, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 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: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684673 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529684673 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684673/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684673/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684673 Building ZINC000529684673 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684673' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684673 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529684673 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684673/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684673 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 485) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2Cc3cc(Cl)ccc3[C@@H]12) `ZINC000529684673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529684673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529684673 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2Cc3cc(Cl)ccc3[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 1, 1, 1, 16, 1, 1, 1, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 9, 9, 1, 9, 9, 1, 1, 1, 1, 9, 9, 9, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 13, 13, 13, 9, 9, 9, 9, 9, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 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: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684673 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684673/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684673 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 486) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2Cc3cc(Cl)ccc3[C@@H]12) `ZINC000529684673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529684673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529684673 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2Cc3cc(Cl)ccc3[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 1, 1, 1, 16, 1, 1, 1, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 1, 9, 9, 1, 1, 1, 1, 10, 10, 10, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 15, 9, 9, 9, 9, 10, 33, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 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: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684673 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529684673 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684673/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684673/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529684673 Building ZINC000529719560 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000529719560 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/487 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1) `ZINC000529719560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529719560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719560 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 24, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/488 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/488' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1) `ZINC000529719560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529719560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719560 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 24, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/489 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/489' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1) `ZINC000529719560.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000529719560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719560 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 24, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/490 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/490' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1) `ZINC000529719560.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000529719560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719560 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 24, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529719560 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 Building ZINC000529719560 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000529719560 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 487) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1) `ZINC000529719560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529719560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719560 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 24, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 488) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1) `ZINC000529719560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529719560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719560 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 24, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 489) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/489: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1) `ZINC000529719560.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000529719560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719560 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 24, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 490) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/490: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1) `ZINC000529719560.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000529719560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719560 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 24, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529719560 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 Building ZINC000529719560 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000529719560 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 487) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1) `ZINC000529719560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529719560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719560 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 24, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 488) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1) `ZINC000529719560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529719560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719560 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 24, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 489) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/489: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1) `ZINC000529719560.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000529719560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719560 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 24, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 490) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/490: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1) `ZINC000529719560.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000529719560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719560 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 24, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529719560 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 Building ZINC000529719560 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000529719560 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 487) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1) `ZINC000529719560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529719560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719560 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 24, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 488) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1) `ZINC000529719560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529719560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719560 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 24, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 489) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/489: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1) `ZINC000529719560.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000529719560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719560 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 24, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 490) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/490: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1) `ZINC000529719560.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000529719560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719560 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 24, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529719560 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719560 Building ZINC000529719561 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000529719561 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/491 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1) `ZINC000529719561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529719561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719561 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 22, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/492 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/492' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1) `ZINC000529719561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529719561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719561 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 22, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 22, 22, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/493 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/493' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1) `ZINC000529719561.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000529719561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719561 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 22, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/494 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/494' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1) `ZINC000529719561.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000529719561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719561 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 22, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 22, 22, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529719561 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 Building ZINC000529719561 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000529719561 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 491) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1) `ZINC000529719561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529719561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719561 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 22, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 492) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1) `ZINC000529719561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529719561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719561 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 22, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 22, 22, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 493) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/493: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1) `ZINC000529719561.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000529719561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719561 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 22, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 494) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/494: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1) `ZINC000529719561.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000529719561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719561 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 22, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 22, 22, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529719561 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 Building ZINC000529719561 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000529719561 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 491) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1) `ZINC000529719561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529719561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719561 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 22, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 492) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1) `ZINC000529719561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529719561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719561 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 22, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 22, 22, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 493) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/493: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1) `ZINC000529719561.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000529719561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719561 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 22, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 494) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/494: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1) `ZINC000529719561.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000529719561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719561 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 22, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 22, 22, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529719561 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 Building ZINC000529719561 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000529719561 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 491) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1) `ZINC000529719561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529719561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719561 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 22, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 492) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1) `ZINC000529719561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529719561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719561 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 22, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 22, 22, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 493) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/493: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1) `ZINC000529719561.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000529719561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719561 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 22, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 494) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/494: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1) `ZINC000529719561.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000529719561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529719561 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C1CCCCC1 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 22, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 22, 22, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529719561 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529719561 Building ZINC000128912641 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000128912641' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000128912641 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000128912641 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000128912641/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000128912641 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/495 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccnc2OCC(F)F)cc1) `ZINC000128912641.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000128912641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000128912641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000128912641 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccnc2OCC(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', '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, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 5, 5, 15, 15, 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, 9, 8, 10, 11, 6, 4, 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: [4, 2, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 19, 41, 49, 49, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 41, 41, 49, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000128912641 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000128912641/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000128912641 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/496 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/496' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccnc2OCC(F)F)cc1) `ZINC000128912641.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000128912641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000128912641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000128912641 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccnc2OCC(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', '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, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 5, 5, 15, 15, 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, 9, 8, 10, 11, 6, 4, 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: [4, 1, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 17, 41, 49, 49, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 41, 41, 49, 4, 4] 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]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000128912641 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000128912641 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000128912641/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000128912641/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000128912641 Building ZINC000128912641 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000128912641' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000128912641 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000128912641 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000128912641/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000128912641 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 495) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccnc2OCC(F)F)cc1) `ZINC000128912641.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000128912641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000128912641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000128912641 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccnc2OCC(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', '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, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 5, 5, 15, 15, 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, 9, 8, 10, 11, 6, 4, 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: [4, 2, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 19, 41, 49, 49, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 41, 41, 49, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000128912641 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000128912641/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000128912641 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 496) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccnc2OCC(F)F)cc1) `ZINC000128912641.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000128912641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000128912641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000128912641 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccnc2OCC(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', '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, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 5, 5, 15, 15, 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, 9, 8, 10, 11, 6, 4, 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: [4, 1, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 17, 41, 49, 49, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 41, 41, 49, 4, 4] 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]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000128912641 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000128912641 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000128912641/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000128912641/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000128912641 Building ZINC000529809122 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529809122' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529809122 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529809122 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529809122/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529809122 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/497 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)OC1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1) `ZINC000529809122.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529809122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529809122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000529809122 none CCC(C)(C)OC1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 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, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 19, 8, 19, 19, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 2, 4, 10, 4, 4, 4, 4, 23, 23, 23, 23, 23, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4, 10, 10, 10, 4, 4, 4] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529809122 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529809122/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529809122 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/498 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/498' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)OC1CN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1) `ZINC000529809122.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529809122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529809122/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000529809122 none CCC(C)(C)OC1CN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 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, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 18, 6, 18, 18, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 2, 22, 22, 22, 22, 22, 18, 18, 18, 18, 18, 18, 2, 2, 2, 4, 4, 8, 8, 8, 4, 2, 2] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529809122 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529809122 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529809122/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529809122/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529809122 Building ZINC000529809122 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529809122' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529809122 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529809122 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529809122/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529809122 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 497) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCC(C)(C)OC1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1) `ZINC000529809122.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529809122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529809122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000529809122 none CCC(C)(C)OC1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 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, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 19, 8, 19, 19, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 2, 4, 10, 4, 4, 4, 4, 23, 23, 23, 23, 23, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4, 10, 10, 10, 4, 4, 4] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529809122 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529809122/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529809122 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 498) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCC(C)(C)OC1CN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1) `ZINC000529809122.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529809122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529809122/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000529809122 none CCC(C)(C)OC1CN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 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, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 18, 6, 18, 18, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 2, 22, 22, 22, 22, 22, 18, 18, 18, 18, 18, 18, 2, 2, 2, 4, 4, 8, 8, 8, 4, 2, 2] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529809122 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529809122 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529809122/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529809122/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529809122 Building ZINC000529824378 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824378' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824378 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529824378 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824378/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824378 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/499 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/499' -> `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](c2ccccn2)C2CCC2)cn1) `ZINC000529824378.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529824378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000529824378 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](c2ccccn2)C2CCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 25, 25, 25, 25, 25, 9, 14, 14, 14, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 4, 25, 25, 25, 25, 14, 14, 14, 14, 14, 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824378 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824378/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824378 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/500 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/500' -> `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](c2ccccn2)C2CCC2)cn1) `ZINC000529824378.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529824378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824378/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000529824378 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](c2ccccn2)C2CCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 24, 24, 24, 24, 24, 9, 12, 12, 12, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 4, 24, 24, 24, 24, 12, 12, 12, 12, 12, 12, 12, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824378 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529824378 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824378/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824378/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824378 Building ZINC000529824378 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824378' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824378 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529824378 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824378/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824378 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 499) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](c2ccccn2)C2CCC2)cn1) `ZINC000529824378.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529824378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000529824378 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](c2ccccn2)C2CCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 25, 25, 25, 25, 25, 9, 14, 14, 14, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 4, 25, 25, 25, 25, 14, 14, 14, 14, 14, 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824378 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824378/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824378 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 500) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](c2ccccn2)C2CCC2)cn1) `ZINC000529824378.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529824378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824378/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000529824378 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](c2ccccn2)C2CCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 24, 24, 24, 24, 24, 9, 12, 12, 12, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 4, 24, 24, 24, 24, 12, 12, 12, 12, 12, 12, 12, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824378 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529824378 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824378/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824378/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824378 Building ZINC000529824379 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824379' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824379 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529824379 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824379/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824379 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/501 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/501' -> `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](c2ccccn2)C2CCC2)cn1) `ZINC000529824379.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529824379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000529824379 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2ccccn2)C2CCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 22, 22, 22, 22, 22, 9, 13, 13, 13, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 4, 22, 22, 22, 22, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824379 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824379/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824379 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/502 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/502' -> `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](c2ccccn2)C2CCC2)cn1) `ZINC000529824379.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529824379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824379/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000529824379 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](c2ccccn2)C2CCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 25, 25, 25, 25, 25, 8, 14, 14, 14, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 4, 25, 25, 25, 25, 14, 14, 14, 14, 14, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824379 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529824379 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824379/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824379/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824379 Building ZINC000529824379 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824379' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824379 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529824379 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824379/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824379 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 501) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2ccccn2)C2CCC2)cn1) `ZINC000529824379.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529824379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000529824379 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2ccccn2)C2CCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 22, 22, 22, 22, 22, 9, 13, 13, 13, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 4, 22, 22, 22, 22, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824379 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824379/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824379 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 502) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](c2ccccn2)C2CCC2)cn1) `ZINC000529824379.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529824379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824379/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000529824379 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](c2ccccn2)C2CCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 25, 25, 25, 25, 25, 8, 14, 14, 14, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 4, 25, 25, 25, 25, 14, 14, 14, 14, 14, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824379 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529824379 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824379/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824379/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529824379 Building ZINC000529835539 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529835539' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529835539 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529835539 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529835539/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529835539 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/503 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)c(OC)c1) `ZINC000529835539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529835539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529835539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000529835539 none COc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 27, 17, 27, 27, 12, 6, 12, 12, 6, 1, 6, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 27, 27, 34, 27, 36, 36, 36, 27, 27, 12, 12, 12, 6, 4, 4, 4, 4, 4, 4, 4, 34, 34, 34, 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]) total number of confs: 156 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529835539 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529835539/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529835539 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/504 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/504' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)c(OC)c1) `ZINC000529835539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529835539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529835539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000529835539 none COc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 26, 26, 26, 26, 12, 6, 12, 12, 6, 1, 6, 1, 1, 1, 6, 6, 2, 6, 6, 6, 6, 26, 26, 33, 26, 37, 37, 37, 26, 26, 12, 12, 12, 6, 6, 6, 6, 6, 6, 6, 6, 33, 33, 33, 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: 125 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529835539 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529835539 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529835539/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529835539/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529835539 Building ZINC000529835539 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529835539' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529835539 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529835539 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529835539/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529835539 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 503) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)c(OC)c1) `ZINC000529835539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529835539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529835539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000529835539 none COc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 27, 17, 27, 27, 12, 6, 12, 12, 6, 1, 6, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 27, 27, 34, 27, 36, 36, 36, 27, 27, 12, 12, 12, 6, 4, 4, 4, 4, 4, 4, 4, 34, 34, 34, 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]) total number of confs: 156 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529835539 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529835539/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529835539 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 504) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)c(OC)c1) `ZINC000529835539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529835539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529835539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000529835539 none COc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 26, 26, 26, 26, 12, 6, 12, 12, 6, 1, 6, 1, 1, 1, 6, 6, 2, 6, 6, 6, 6, 26, 26, 33, 26, 37, 37, 37, 26, 26, 12, 12, 12, 6, 6, 6, 6, 6, 6, 6, 6, 33, 33, 33, 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: 125 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529835539 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529835539 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529835539/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529835539/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529835539 Building ZINC000529842383 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529842383' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529842383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529842383 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529842383/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529842383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/505 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1cncc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000529842383.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529842383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529842383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000529842383 none CCCOc1cncc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 21, 21, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 8, 38, 38, 38, 38, 38, 21, 21, 8, 8, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 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, 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/83235/xao-8058115.15/working/building/ZINC000529842383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529842383/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529842383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/506 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/506' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1cncc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000529842383.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529842383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529842383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000529842383 none CCCOc1cncc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 8, 34, 34, 34, 34, 34, 20, 20, 8, 8, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 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, 45]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529842383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529842383 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529842383/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529842383/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529842383 Building ZINC000529842383 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529842383' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529842383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529842383 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529842383/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529842383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 505) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCCOc1cncc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000529842383.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529842383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529842383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000529842383 none CCCOc1cncc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 21, 21, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 8, 38, 38, 38, 38, 38, 21, 21, 8, 8, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 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, 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/83235/xao-8058115.15/working/building/ZINC000529842383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529842383/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529842383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 506) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCCOc1cncc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000529842383.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529842383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529842383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000529842383 none CCCOc1cncc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 8, 34, 34, 34, 34, 34, 20, 20, 8, 8, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 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, 45]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529842383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529842383 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529842383/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529842383/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529842383 Building ZINC000529845388 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529845388' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529845388 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529845388 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529845388/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529845388 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/507 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C)cc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000529845388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529845388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529845388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000529845388 none COc1c(C)cc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 21, 21, 21, 21, 7, 21, 21, 21, 7, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 21, 21, 21, 21, 21, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 98 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529845388 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529845388/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529845388 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/508 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/508' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C)cc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000529845388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529845388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529845388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000529845388 none COc1c(C)cc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 21, 21, 21, 21, 6, 21, 21, 21, 6, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 21, 21, 21, 11, 21, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 89 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529845388 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529845388 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529845388/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529845388/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529845388 Building ZINC000529845388 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529845388' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529845388 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529845388 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529845388/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529845388 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 507) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/507: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C)cc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000529845388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529845388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529845388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000529845388 none COc1c(C)cc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 21, 21, 21, 21, 7, 21, 21, 21, 7, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 21, 21, 21, 21, 21, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 98 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529845388 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529845388/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529845388 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 508) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C)cc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000529845388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529845388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529845388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000529845388 none COc1c(C)cc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 21, 21, 21, 21, 6, 21, 21, 21, 6, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 21, 21, 21, 11, 21, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 89 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529845388 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529845388 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529845388/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529845388/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529845388 Building ZINC000529863073 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529863073' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529863073 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529863073 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529863073/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529863073 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/509 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(Cc3ccco3)C2)cc1Cl) `ZINC000529863073.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529863073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529863073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000529863073 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(Cc3ccco3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 16, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 4, 4, 4, 14, 26, 26, 26, 26, 4, 2, 2, 2, 4, 4, 4, 2, 2, 4, 4, 4, 14, 14, 26, 26, 26, 4, 4, 2] 50 rigid atoms, others: [8, 9, 5, 6, 7] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529863073 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529863073/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529863073 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/510 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/510' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(Cc3ccco3)C2)cc1Cl) `ZINC000529863073.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529863073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529863073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000529863073 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(Cc3ccco3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 16, 7, 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, 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: [7, 4, 2, 4, 4, 1, 1, 1, 1, 1, 2, 4, 4, 4, 14, 25, 25, 25, 25, 4, 4, 4, 4, 7, 7, 7, 4, 4, 4, 4, 4, 14, 14, 25, 25, 25, 4, 4, 4] 50 rigid atoms, others: [8, 9, 5, 6, 7] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 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: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529863073 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529863073 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529863073/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529863073/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529863073 Building ZINC000529863073 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529863073' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529863073 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529863073 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529863073/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529863073 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 509) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(Cc3ccco3)C2)cc1Cl) `ZINC000529863073.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529863073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529863073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000529863073 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(Cc3ccco3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 16, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 4, 4, 4, 14, 26, 26, 26, 26, 4, 2, 2, 2, 4, 4, 4, 2, 2, 4, 4, 4, 14, 14, 26, 26, 26, 4, 4, 2] 50 rigid atoms, others: [8, 9, 5, 6, 7] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529863073 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529863073/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529863073 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 510) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(Cc3ccco3)C2)cc1Cl) `ZINC000529863073.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529863073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529863073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000529863073 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(Cc3ccco3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 16, 7, 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, 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: [7, 4, 2, 4, 4, 1, 1, 1, 1, 1, 2, 4, 4, 4, 14, 25, 25, 25, 25, 4, 4, 4, 4, 7, 7, 7, 4, 4, 4, 4, 4, 14, 14, 25, 25, 25, 4, 4, 4] 50 rigid atoms, others: [8, 9, 5, 6, 7] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 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: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529863073 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529863073 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529863073/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529863073/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529863073 Building ZINC000529861177 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529861177' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529861177 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529861177 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529861177/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529861177 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/511 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(Cc2ccco2)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529861177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529861177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529861177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000529861177 none O=C(N1CC(Cc2ccco2)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.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, 5, 5, 1, 1, 1, 1, 12, 5, 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: [6, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 13, 13, 13, 29, 50, 50, 50, 50, 13, 1, 1, 1, 3, 3, 1, 3, 3, 3, 13, 13, 13, 29, 29, 50, 50, 50, 13, 13, 3, 3, 3, 3] 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: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529861177 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529861177/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529861177 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/512 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/512' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(Cc2ccco2)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529861177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529861177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529861177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000529861177 none O=C(N1CC(Cc2ccco2)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.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, 5, 5, 1, 1, 1, 1, 12, 5, 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: [6, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 15, 15, 15, 28, 50, 50, 50, 50, 15, 1, 1, 1, 2, 2, 1, 1, 2, 2, 15, 15, 15, 28, 28, 50, 50, 50, 15, 15, 2, 2, 2, 2] 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: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529861177 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529861177 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529861177/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529861177/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529861177 Building ZINC000529861177 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529861177' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529861177 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529861177 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529861177/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529861177 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 511) grep: /scratch/xiaobo/83235/xao-8058115.15/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(N1CC(Cc2ccco2)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529861177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529861177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529861177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000529861177 none O=C(N1CC(Cc2ccco2)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.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, 5, 5, 1, 1, 1, 1, 12, 5, 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: [6, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 13, 13, 13, 29, 50, 50, 50, 50, 13, 1, 1, 1, 3, 3, 1, 3, 3, 3, 13, 13, 13, 29, 29, 50, 50, 50, 13, 13, 3, 3, 3, 3] 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: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529861177 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529861177/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529861177 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 512) grep: /scratch/xiaobo/83235/xao-8058115.15/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(N1CC(Cc2ccco2)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529861177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529861177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529861177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000529861177 none O=C(N1CC(Cc2ccco2)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.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, 5, 5, 1, 1, 1, 1, 12, 5, 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: [6, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 15, 15, 15, 28, 50, 50, 50, 50, 15, 1, 1, 1, 2, 2, 1, 1, 2, 2, 15, 15, 15, 28, 28, 50, 50, 50, 15, 15, 2, 2, 2, 2] 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: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529861177 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529861177 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529861177/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529861177/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529861177 Building ZINC000529878566 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529878566' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529878566 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529878566 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529878566/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529878566 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/513 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCc1cc(F)c(Br)cc1F) `ZINC000529878566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529878566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529878566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000529878566 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCc1cc(F)c(Br)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 15, 1, 17, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 4, 23, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 23, 23, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529878566 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529878566/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529878566 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/514 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/514' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCc1cc(F)c(Br)cc1F) `ZINC000529878566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529878566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529878566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000529878566 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCc1cc(F)c(Br)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 15, 1, 17, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 4, 20, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 20, 20, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529878566 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529878566 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529878566/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529878566/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529878566 Building ZINC000529878566 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529878566' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529878566 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529878566 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529878566/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529878566 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 513) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCc1cc(F)c(Br)cc1F) `ZINC000529878566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529878566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529878566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000529878566 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCc1cc(F)c(Br)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 15, 1, 17, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 4, 23, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 23, 23, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529878566 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529878566/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529878566 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 514) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCc1cc(F)c(Br)cc1F) `ZINC000529878566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529878566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529878566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000529878566 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCc1cc(F)c(Br)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 15, 1, 17, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 4, 20, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 20, 20, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529878566 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529878566 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529878566/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529878566/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529878566 Building ZINC000529887927 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529887927' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529887927 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529887927 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529887927/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529887927 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/515 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCc2c(cccc2C(F)(F)F)C1) `ZINC000529887927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529887927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529887927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000529887927 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCc2c(cccc2C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 1, 1, 1, 1, 6, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 9, 9, 9, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529887927 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529887927/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529887927 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/516 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/516' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCc2c(cccc2C(F)(F)F)C1) `ZINC000529887927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529887927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529887927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000529887927 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCc2c(cccc2C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 1, 1, 1, 1, 6, 11, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529887927 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529887927 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529887927/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529887927/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529887927 Building ZINC000529887927 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529887927' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529887927 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529887927 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529887927/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529887927 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 515) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCc2c(cccc2C(F)(F)F)C1) `ZINC000529887927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529887927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529887927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000529887927 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCc2c(cccc2C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 1, 1, 1, 1, 6, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 9, 9, 9, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529887927 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529887927/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529887927 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 516) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCc2c(cccc2C(F)(F)F)C1) `ZINC000529887927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529887927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529887927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000529887927 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCc2c(cccc2C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 1, 1, 1, 1, 6, 11, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529887927 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529887927 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529887927/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529887927/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529887927 Building ZINC000529935646 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529935646' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529935646 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529935646 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529935646/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529935646 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/517 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C3CCOCC3)c2)cn1) `ZINC000529935646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529935646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529935646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000529935646 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C3CCOCC3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 2, 8, 8, 16, 16, 16, 16, 16, 8, 5, 5, 10, 10, 10, 10, 10, 5, 2, 8, 8, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529935646 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529935646/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529935646 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/518 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/518' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C3CCOCC3)c2)cn1) `ZINC000529935646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529935646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529935646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000529935646 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C3CCOCC3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 2, 8, 8, 17, 17, 17, 17, 17, 8, 5, 5, 10, 10, 10, 10, 10, 5, 2, 8, 8, 2, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529935646 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529935646 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529935646/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529935646/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529935646 Building ZINC000529935646 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529935646' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529935646 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529935646 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529935646/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529935646 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 517) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C3CCOCC3)c2)cn1) `ZINC000529935646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529935646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529935646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000529935646 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C3CCOCC3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 2, 8, 8, 16, 16, 16, 16, 16, 8, 5, 5, 10, 10, 10, 10, 10, 5, 2, 8, 8, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529935646 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529935646/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529935646 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 518) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C3CCOCC3)c2)cn1) `ZINC000529935646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529935646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529935646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000529935646 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C3CCOCC3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 2, 8, 8, 17, 17, 17, 17, 17, 8, 5, 5, 10, 10, 10, 10, 10, 5, 2, 8, 8, 2, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529935646 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529935646 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529935646/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529935646/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529935646 Building ZINC000529942275 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529942275' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529942275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529942275 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529942275/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529942275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/519 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Cl)ccc1C1=CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000529942275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529942275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529942275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000529942275 none Cc1cc(Cl)ccc1C1=CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 32, 32, 17, 17, 17, 17, 8, 2, 12, 1, 1, 1, 6, 6, 6, 6, 6, 17, 17, 32, 32, 32, 32, 32, 32, 17, 17, 17, 6, 6, 6, 6, 6, 17, 17, 17, 17] 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: 79 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529942275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529942275/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529942275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/520 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/520' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Cl)ccc1C1=CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000529942275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529942275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529942275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000529942275 none Cc1cc(Cl)ccc1C1=CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 16, 32, 32, 16, 16, 16, 16, 8, 2, 11, 1, 1, 1, 6, 6, 6, 6, 6, 16, 16, 32, 32, 32, 32, 32, 32, 16, 16, 16, 6, 6, 6, 6, 6, 16, 16, 16, 16] 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: 97 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529942275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529942275 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529942275/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529942275/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529942275 Building ZINC000529942275 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529942275' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529942275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529942275 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529942275/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529942275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 519) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1cc(Cl)ccc1C1=CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000529942275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529942275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529942275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000529942275 none Cc1cc(Cl)ccc1C1=CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 32, 32, 17, 17, 17, 17, 8, 2, 12, 1, 1, 1, 6, 6, 6, 6, 6, 17, 17, 32, 32, 32, 32, 32, 32, 17, 17, 17, 6, 6, 6, 6, 6, 17, 17, 17, 17] 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: 79 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529942275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529942275/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529942275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 520) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1cc(Cl)ccc1C1=CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000529942275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529942275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529942275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000529942275 none Cc1cc(Cl)ccc1C1=CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 16, 32, 32, 16, 16, 16, 16, 8, 2, 11, 1, 1, 1, 6, 6, 6, 6, 6, 16, 16, 32, 32, 32, 32, 32, 32, 16, 16, 16, 6, 6, 6, 6, 6, 16, 16, 16, 16] 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: 97 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529942275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529942275 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529942275/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529942275/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529942275 Building ZINC000529947966 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947966' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947966 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529947966 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947966/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947966 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/521 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](c3ccc(F)cc3)C2(C)C)cn1) `ZINC000529947966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529947966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000529947966 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](c3ccc(F)cc3)C2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 10, 10, 17, 17, 17, 17, 17, 23, 23, 17, 17, 23, 23, 17, 17, 17, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 23, 23, 23, 23, 17, 17, 17, 17, 17, 17, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 72 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947966 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947966/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947966 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/522 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/522' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](c3ccc(F)cc3)C2(C)C)cn1) `ZINC000529947966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529947966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000529947966 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](c3ccc(F)cc3)C2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 10, 10, 17, 17, 17, 17, 17, 22, 22, 17, 17, 22, 22, 17, 17, 17, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 22, 22, 22, 22, 17, 17, 17, 17, 17, 17, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 70 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947966 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529947966 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947966/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947966/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947966 Building ZINC000529947966 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947966' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947966 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529947966 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947966/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947966 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 521) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](c3ccc(F)cc3)C2(C)C)cn1) `ZINC000529947966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529947966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000529947966 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](c3ccc(F)cc3)C2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 10, 10, 17, 17, 17, 17, 17, 23, 23, 17, 17, 23, 23, 17, 17, 17, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 23, 23, 23, 23, 17, 17, 17, 17, 17, 17, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 72 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947966 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947966/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947966 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 522) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](c3ccc(F)cc3)C2(C)C)cn1) `ZINC000529947966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529947966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000529947966 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](c3ccc(F)cc3)C2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 10, 10, 17, 17, 17, 17, 17, 22, 22, 17, 17, 22, 22, 17, 17, 17, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 22, 22, 22, 22, 17, 17, 17, 17, 17, 17, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 70 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947966 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529947966 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947966/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947966/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947966 Building ZINC000529947967 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947967' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947967 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529947967 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947967/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947967 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/523 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](c3ccc(F)cc3)C2(C)C)cn1) `ZINC000529947967.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529947967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000529947967 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](c3ccc(F)cc3)C2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 7, 10, 17, 17, 17, 17, 17, 22, 22, 17, 22, 22, 22, 17, 17, 17, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 22, 22, 22, 22, 17, 17, 17, 17, 17, 17, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 77 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947967 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947967/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947967 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/524 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/524' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](c3ccc(F)cc3)C2(C)C)cn1) `ZINC000529947967.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529947967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947967/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000529947967 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](c3ccc(F)cc3)C2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 6, 10, 17, 17, 17, 17, 17, 24, 24, 19, 24, 24, 24, 17, 17, 17, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 24, 24, 24, 24, 17, 17, 17, 17, 17, 17, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 77 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947967 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529947967 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947967/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947967/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947967 Building ZINC000529947967 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947967' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947967 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529947967 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947967/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947967 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 523) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](c3ccc(F)cc3)C2(C)C)cn1) `ZINC000529947967.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529947967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000529947967 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](c3ccc(F)cc3)C2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 7, 10, 17, 17, 17, 17, 17, 22, 22, 17, 22, 22, 22, 17, 17, 17, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 22, 22, 22, 22, 17, 17, 17, 17, 17, 17, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 77 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947967 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947967/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947967 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 524) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](c3ccc(F)cc3)C2(C)C)cn1) `ZINC000529947967.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529947967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947967/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000529947967 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](c3ccc(F)cc3)C2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 6, 10, 17, 17, 17, 17, 17, 24, 24, 19, 24, 24, 24, 17, 17, 17, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 24, 24, 24, 24, 17, 17, 17, 17, 17, 17, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 77 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947967 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529947967 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947967/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947967/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529947967 Building ZINC000529986435 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986435' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986435 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529986435 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986435/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986435 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/525 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1O[C@@H](C)[C@@H](C)[C@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529986435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529986435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000529986435 none C[C@H]1O[C@@H](C)[C@@H](C)[C@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.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', '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, 12, 5, 7, 5, 5, 7, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 19, 38, 10, 1, 10, 1, 1, 1, 6, 6, 1, 1, 6, 6, 38, 38, 38, 38, 38, 38, 38, 38, 38, 10, 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, 36, 37]) total number of confs: 118 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986435 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986435/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986435 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/526 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/526' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1O[C@@H](C)[C@@H](C)[C@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529986435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529986435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000529986435 none C[C@H]1O[C@@H](C)[C@@H](C)[C@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.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', '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, 12, 5, 7, 5, 5, 7, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 19, 37, 11, 1, 11, 1, 1, 1, 6, 6, 1, 4, 6, 6, 37, 37, 37, 37, 37, 37, 37, 37, 37, 11, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986435 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529986435 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986435/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986435/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986435 Building ZINC000529986435 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986435' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986435 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529986435 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986435/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986435 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 525) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H]1O[C@@H](C)[C@@H](C)[C@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529986435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529986435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000529986435 none C[C@H]1O[C@@H](C)[C@@H](C)[C@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.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', '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, 12, 5, 7, 5, 5, 7, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 19, 38, 10, 1, 10, 1, 1, 1, 6, 6, 1, 1, 6, 6, 38, 38, 38, 38, 38, 38, 38, 38, 38, 10, 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, 36, 37]) total number of confs: 118 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986435 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986435/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986435 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 526) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H]1O[C@@H](C)[C@@H](C)[C@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529986435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529986435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000529986435 none C[C@H]1O[C@@H](C)[C@@H](C)[C@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.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', '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, 12, 5, 7, 5, 5, 7, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 19, 37, 11, 1, 11, 1, 1, 1, 6, 6, 1, 4, 6, 6, 37, 37, 37, 37, 37, 37, 37, 37, 37, 11, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986435 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529986435 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986435/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986435/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986435 Building ZINC000529986438 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986438' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986438 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529986438 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986438/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986438 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/527 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1O[C@@H](C)[C@@H](C)[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529986438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529986438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000529986438 none C[C@H]1O[C@@H](C)[C@@H](C)[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.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', '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, 12, 5, 7, 5, 5, 7, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 31, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 8, 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, 36, 37]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986438 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986438/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986438 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/528 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/528' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1O[C@@H](C)[C@@H](C)[C@@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529986438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529986438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000529986438 none C[C@H]1O[C@@H](C)[C@@H](C)[C@@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.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', '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, 12, 5, 7, 5, 5, 7, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 12, 31, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 7, 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, 36, 37]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986438 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529986438 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986438/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986438/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986438 Building ZINC000529986438 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986438' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986438 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529986438 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986438/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986438 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 527) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H]1O[C@@H](C)[C@@H](C)[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529986438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529986438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000529986438 none C[C@H]1O[C@@H](C)[C@@H](C)[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.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', '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, 12, 5, 7, 5, 5, 7, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 31, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 8, 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, 36, 37]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986438 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986438/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986438 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 528) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H]1O[C@@H](C)[C@@H](C)[C@@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529986438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529986438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000529986438 none C[C@H]1O[C@@H](C)[C@@H](C)[C@@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.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', '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, 12, 5, 7, 5, 5, 7, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 12, 31, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 7, 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, 36, 37]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986438 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529986438 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986438/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986438/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986438 Building ZINC000529986440 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986440' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986440 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529986440 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986440/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986440 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/529 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/529' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1O[C@@H](C)[C@H](C)[C@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529986440.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529986440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000529986440 none C[C@H]1O[C@@H](C)[C@H](C)[C@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.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', '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, 12, 5, 7, 5, 5, 7, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 31, 8, 1, 8, 1, 1, 1, 6, 6, 1, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 8, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986440 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986440/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986440 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/530 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/530' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1O[C@@H](C)[C@H](C)[C@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529986440.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529986440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986440/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000529986440 none C[C@H]1O[C@@H](C)[C@H](C)[C@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.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', '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, 12, 5, 7, 5, 5, 7, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 18, 38, 10, 1, 10, 1, 1, 1, 6, 6, 1, 1, 6, 6, 38, 38, 38, 38, 38, 38, 38, 38, 38, 10, 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, 36, 37]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986440 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529986440 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986440/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986440/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986440 Building ZINC000529986440 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986440' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986440 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529986440 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986440/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986440 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 529) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H]1O[C@@H](C)[C@H](C)[C@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529986440.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529986440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000529986440 none C[C@H]1O[C@@H](C)[C@H](C)[C@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.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', '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, 12, 5, 7, 5, 5, 7, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 31, 8, 1, 8, 1, 1, 1, 6, 6, 1, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 8, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986440 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986440/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986440 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 530) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H]1O[C@@H](C)[C@H](C)[C@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529986440.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529986440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986440/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000529986440 none C[C@H]1O[C@@H](C)[C@H](C)[C@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.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', '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, 12, 5, 7, 5, 5, 7, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 18, 38, 10, 1, 10, 1, 1, 1, 6, 6, 1, 1, 6, 6, 38, 38, 38, 38, 38, 38, 38, 38, 38, 10, 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, 36, 37]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986440 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529986440 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986440/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986440/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986440 Building ZINC000529986443 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986443' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986443 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529986443 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986443/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986443 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/531 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1O[C@@H](C)[C@H](C)[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529986443.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529986443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000529986443 none C[C@H]1O[C@@H](C)[C@H](C)[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.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', '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, 12, 5, 7, 5, 5, 7, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 16, 32, 8, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 32, 32, 32, 32, 32, 32, 32, 32, 32, 8, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986443 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986443/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986443 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/532 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/532' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1O[C@@H](C)[C@H](C)[C@@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529986443.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529986443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986443/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000529986443 none C[C@H]1O[C@@H](C)[C@H](C)[C@@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.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', '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, 12, 5, 7, 5, 5, 7, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 17, 34, 9, 1, 9, 1, 1, 1, 6, 6, 1, 1, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34, 9, 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, 36, 37]) total number of confs: 106 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986443 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529986443 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986443/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986443/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986443 Building ZINC000529986443 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986443' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986443 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529986443 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986443/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986443 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 531) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H]1O[C@@H](C)[C@H](C)[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529986443.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529986443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000529986443 none C[C@H]1O[C@@H](C)[C@H](C)[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.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', '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, 12, 5, 7, 5, 5, 7, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 16, 32, 8, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 32, 32, 32, 32, 32, 32, 32, 32, 32, 8, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986443 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986443/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986443 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 532) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H]1O[C@@H](C)[C@H](C)[C@@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000529986443.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529986443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986443/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000529986443 none C[C@H]1O[C@@H](C)[C@H](C)[C@@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.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', '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, 12, 5, 7, 5, 5, 7, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 17, 34, 9, 1, 9, 1, 1, 1, 6, 6, 1, 1, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34, 9, 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, 36, 37]) total number of confs: 106 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986443 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000529986443 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986443/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986443/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000529986443 Building ZINC000530036161 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036161' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036161 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000530036161 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036161/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036161 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/533 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](c3cccc(F)c3)C2(C)C)cn1) `ZINC000530036161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530036161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000530036161 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](c3cccc(F)c3)C2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 11, 11, 11, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 54 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036161 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036161/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036161 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/534 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/534' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](c3cccc(F)c3)C2(C)C)cn1) `ZINC000530036161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530036161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000530036161 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](c3cccc(F)c3)C2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 13, 28, 28, 28, 28, 28, 28, 13, 13, 13, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 28, 28, 28, 28, 13, 13, 13, 13, 13, 13, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 57 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036161 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000530036161 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036161/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036161/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036161 Building ZINC000530036161 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036161' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036161 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000530036161 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036161/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036161 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 533) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](c3cccc(F)c3)C2(C)C)cn1) `ZINC000530036161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530036161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000530036161 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](c3cccc(F)c3)C2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 11, 11, 11, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 54 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036161 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036161/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036161 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 534) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](c3cccc(F)c3)C2(C)C)cn1) `ZINC000530036161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530036161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000530036161 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](c3cccc(F)c3)C2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 13, 28, 28, 28, 28, 28, 28, 13, 13, 13, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 28, 28, 28, 28, 13, 13, 13, 13, 13, 13, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 57 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036161 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000530036161 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036161/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036161/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036161 Building ZINC000530036162 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036162' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036162 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000530036162 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036162/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036162 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/535 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](c3cccc(F)c3)C2(C)C)cn1) `ZINC000530036162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530036162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000530036162 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](c3cccc(F)c3)C2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 4, 7, 13, 13, 13, 13, 13, 28, 28, 28, 28, 28, 28, 13, 13, 13, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 28, 28, 28, 28, 13, 13, 13, 13, 13, 13, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 54 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036162 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036162/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036162 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/536 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/536' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](c3cccc(F)c3)C2(C)C)cn1) `ZINC000530036162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530036162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000530036162 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](c3cccc(F)c3)C2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 6, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 11, 11, 11, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 52 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036162 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000530036162 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036162/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036162/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036162 Building ZINC000530036162 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036162' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036162 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000530036162 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036162/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036162 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 535) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](c3cccc(F)c3)C2(C)C)cn1) `ZINC000530036162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530036162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000530036162 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](c3cccc(F)c3)C2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 4, 7, 13, 13, 13, 13, 13, 28, 28, 28, 28, 28, 28, 13, 13, 13, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 28, 28, 28, 28, 13, 13, 13, 13, 13, 13, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 54 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036162 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036162/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036162 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 536) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](c3cccc(F)c3)C2(C)C)cn1) `ZINC000530036162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530036162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000530036162 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](c3cccc(F)c3)C2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 6, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 11, 11, 11, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 52 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036162 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000530036162 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036162/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036162/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530036162 Building ZINC000530029856 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000530029856 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/537 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530029856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029856 none O=C(NC[C@H]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 21, 34, 34, 34, 34, 36, 40, 40, 40, 40, 1, 1, 1, 6, 6, 6, 6, 6, 4, 17, 17, 34, 34, 34, 34, 40, 40, 40, 40, 40, 40, 40, 40, 40, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/538 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/538' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530029856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029856 none O=C(NC[C@H]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 20, 33, 33, 33, 33, 34, 38, 38, 38, 38, 1, 1, 1, 7, 7, 7, 7, 7, 3, 17, 17, 33, 33, 33, 33, 38, 38, 38, 38, 38, 38, 38, 38, 38, 7, 7] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/539 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/539' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029856.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000530029856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029856 none O=C(NC[C@H]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 21, 34, 34, 34, 34, 36, 40, 40, 40, 40, 1, 1, 1, 6, 6, 6, 6, 6, 4, 17, 17, 34, 34, 34, 34, 40, 40, 40, 40, 40, 40, 40, 40, 40, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/540 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/540' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029856.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000530029856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029856 none O=C(NC[C@H]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 20, 33, 33, 33, 33, 34, 38, 38, 38, 38, 1, 1, 1, 7, 7, 7, 7, 7, 3, 17, 17, 33, 33, 33, 33, 38, 38, 38, 38, 38, 38, 38, 38, 38, 7, 7] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000530029856 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 Building ZINC000530029856 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000530029856 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 537) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NC[C@H]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530029856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029856 none O=C(NC[C@H]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 21, 34, 34, 34, 34, 36, 40, 40, 40, 40, 1, 1, 1, 6, 6, 6, 6, 6, 4, 17, 17, 34, 34, 34, 34, 40, 40, 40, 40, 40, 40, 40, 40, 40, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 538) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NC[C@H]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530029856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029856 none O=C(NC[C@H]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 20, 33, 33, 33, 33, 34, 38, 38, 38, 38, 1, 1, 1, 7, 7, 7, 7, 7, 3, 17, 17, 33, 33, 33, 33, 38, 38, 38, 38, 38, 38, 38, 38, 38, 7, 7] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 539) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/539: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029856.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000530029856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029856 none O=C(NC[C@H]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 21, 34, 34, 34, 34, 36, 40, 40, 40, 40, 1, 1, 1, 6, 6, 6, 6, 6, 4, 17, 17, 34, 34, 34, 34, 40, 40, 40, 40, 40, 40, 40, 40, 40, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 540) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029856.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000530029856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029856 none O=C(NC[C@H]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 20, 33, 33, 33, 33, 34, 38, 38, 38, 38, 1, 1, 1, 7, 7, 7, 7, 7, 3, 17, 17, 33, 33, 33, 33, 38, 38, 38, 38, 38, 38, 38, 38, 38, 7, 7] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000530029856 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 Building ZINC000530029856 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000530029856 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 537) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NC[C@H]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530029856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029856 none O=C(NC[C@H]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 21, 34, 34, 34, 34, 36, 40, 40, 40, 40, 1, 1, 1, 6, 6, 6, 6, 6, 4, 17, 17, 34, 34, 34, 34, 40, 40, 40, 40, 40, 40, 40, 40, 40, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 538) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NC[C@H]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530029856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029856 none O=C(NC[C@H]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 20, 33, 33, 33, 33, 34, 38, 38, 38, 38, 1, 1, 1, 7, 7, 7, 7, 7, 3, 17, 17, 33, 33, 33, 33, 38, 38, 38, 38, 38, 38, 38, 38, 38, 7, 7] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 539) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/539: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029856.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000530029856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029856 none O=C(NC[C@H]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 21, 34, 34, 34, 34, 36, 40, 40, 40, 40, 1, 1, 1, 6, 6, 6, 6, 6, 4, 17, 17, 34, 34, 34, 34, 40, 40, 40, 40, 40, 40, 40, 40, 40, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 540) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029856.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000530029856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029856 none O=C(NC[C@H]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 20, 33, 33, 33, 33, 34, 38, 38, 38, 38, 1, 1, 1, 7, 7, 7, 7, 7, 3, 17, 17, 33, 33, 33, 33, 38, 38, 38, 38, 38, 38, 38, 38, 38, 7, 7] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000530029856 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 Building ZINC000530029856 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000530029856 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 537) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NC[C@H]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530029856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029856 none O=C(NC[C@H]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 21, 34, 34, 34, 34, 36, 40, 40, 40, 40, 1, 1, 1, 6, 6, 6, 6, 6, 4, 17, 17, 34, 34, 34, 34, 40, 40, 40, 40, 40, 40, 40, 40, 40, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 538) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NC[C@H]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530029856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029856 none O=C(NC[C@H]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 20, 33, 33, 33, 33, 34, 38, 38, 38, 38, 1, 1, 1, 7, 7, 7, 7, 7, 3, 17, 17, 33, 33, 33, 33, 38, 38, 38, 38, 38, 38, 38, 38, 38, 7, 7] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 539) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/539: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029856.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000530029856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029856 none O=C(NC[C@H]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 21, 34, 34, 34, 34, 36, 40, 40, 40, 40, 1, 1, 1, 6, 6, 6, 6, 6, 4, 17, 17, 34, 34, 34, 34, 40, 40, 40, 40, 40, 40, 40, 40, 40, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 540) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029856.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000530029856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029856 none O=C(NC[C@H]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 20, 33, 33, 33, 33, 34, 38, 38, 38, 38, 1, 1, 1, 7, 7, 7, 7, 7, 3, 17, 17, 33, 33, 33, 33, 38, 38, 38, 38, 38, 38, 38, 38, 38, 7, 7] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000530029856 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029856 Building ZINC000530029857 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000530029857 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/541 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530029857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029857 none O=C(NC[C@@H]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 19, 34, 34, 34, 34, 36, 38, 38, 38, 38, 1, 1, 1, 6, 6, 6, 6, 6, 3, 17, 17, 34, 34, 34, 34, 38, 38, 38, 38, 38, 38, 38, 38, 38, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/542 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/542' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530029857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029857 none O=C(NC[C@@H]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 21, 36, 36, 36, 36, 38, 38, 38, 38, 38, 1, 1, 1, 9, 9, 9, 9, 9, 4, 17, 17, 36, 36, 36, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/543 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/543' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029857.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000530029857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029857 none O=C(NC[C@@H]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 19, 34, 34, 34, 34, 36, 38, 38, 38, 38, 1, 1, 1, 6, 6, 6, 6, 6, 3, 17, 17, 34, 34, 34, 34, 38, 38, 38, 38, 38, 38, 38, 38, 38, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/544 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/544' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029857.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000530029857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029857 none O=C(NC[C@@H]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 21, 36, 36, 36, 36, 38, 38, 38, 38, 38, 1, 1, 1, 9, 9, 9, 9, 9, 4, 17, 17, 36, 36, 36, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000530029857 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 Building ZINC000530029857 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000530029857 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 541) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NC[C@@H]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530029857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029857 none O=C(NC[C@@H]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 19, 34, 34, 34, 34, 36, 38, 38, 38, 38, 1, 1, 1, 6, 6, 6, 6, 6, 3, 17, 17, 34, 34, 34, 34, 38, 38, 38, 38, 38, 38, 38, 38, 38, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 542) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NC[C@@H]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530029857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029857 none O=C(NC[C@@H]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 21, 36, 36, 36, 36, 38, 38, 38, 38, 38, 1, 1, 1, 9, 9, 9, 9, 9, 4, 17, 17, 36, 36, 36, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 543) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029857.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000530029857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029857 none O=C(NC[C@@H]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 19, 34, 34, 34, 34, 36, 38, 38, 38, 38, 1, 1, 1, 6, 6, 6, 6, 6, 3, 17, 17, 34, 34, 34, 34, 38, 38, 38, 38, 38, 38, 38, 38, 38, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 544) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029857.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000530029857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029857 none O=C(NC[C@@H]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 21, 36, 36, 36, 36, 38, 38, 38, 38, 38, 1, 1, 1, 9, 9, 9, 9, 9, 4, 17, 17, 36, 36, 36, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000530029857 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 Building ZINC000530029857 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000530029857 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 541) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NC[C@@H]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530029857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029857 none O=C(NC[C@@H]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 19, 34, 34, 34, 34, 36, 38, 38, 38, 38, 1, 1, 1, 6, 6, 6, 6, 6, 3, 17, 17, 34, 34, 34, 34, 38, 38, 38, 38, 38, 38, 38, 38, 38, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 542) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NC[C@@H]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530029857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029857 none O=C(NC[C@@H]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 21, 36, 36, 36, 36, 38, 38, 38, 38, 38, 1, 1, 1, 9, 9, 9, 9, 9, 4, 17, 17, 36, 36, 36, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 543) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029857.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000530029857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029857 none O=C(NC[C@@H]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 19, 34, 34, 34, 34, 36, 38, 38, 38, 38, 1, 1, 1, 6, 6, 6, 6, 6, 3, 17, 17, 34, 34, 34, 34, 38, 38, 38, 38, 38, 38, 38, 38, 38, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 544) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029857.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000530029857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029857 none O=C(NC[C@@H]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 21, 36, 36, 36, 36, 38, 38, 38, 38, 38, 1, 1, 1, 9, 9, 9, 9, 9, 4, 17, 17, 36, 36, 36, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000530029857 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 Building ZINC000530029857 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000530029857 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 541) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NC[C@@H]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530029857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029857 none O=C(NC[C@@H]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 19, 34, 34, 34, 34, 36, 38, 38, 38, 38, 1, 1, 1, 6, 6, 6, 6, 6, 3, 17, 17, 34, 34, 34, 34, 38, 38, 38, 38, 38, 38, 38, 38, 38, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 542) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NC[C@@H]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530029857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029857 none O=C(NC[C@@H]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 21, 36, 36, 36, 36, 38, 38, 38, 38, 38, 1, 1, 1, 9, 9, 9, 9, 9, 4, 17, 17, 36, 36, 36, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 543) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029857.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000530029857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029857 none O=C(NC[C@@H]1CCN1C1CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 19, 34, 34, 34, 34, 36, 38, 38, 38, 38, 1, 1, 1, 6, 6, 6, 6, 6, 3, 17, 17, 34, 34, 34, 34, 38, 38, 38, 38, 38, 38, 38, 38, 38, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 544) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000530029857.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000530029857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000530029857 none O=C(NC[C@@H]1CCN1C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 21, 36, 36, 36, 36, 38, 38, 38, 38, 38, 1, 1, 1, 9, 9, 9, 9, 9, 4, 17, 17, 36, 36, 36, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000530029857 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530029857 Building ZINC000530043545 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530043545' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530043545 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000530043545 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530043545/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530043545 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/545 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc3c2OC(C)(C)CC3)cn1) `ZINC000530043545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530043545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530043545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000530043545 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc3c2OC(C)(C)CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 13, 13, 13, 7, 13, 13, 13, 13, 13, 13, 6, 6, 10, 10, 10, 10, 10, 6, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530043545 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530043545/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530043545 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/546 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/546' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc3c2OC(C)(C)CC3)cn1) `ZINC000530043545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530043545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530043545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000530043545 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc3c2OC(C)(C)CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 12, 12, 12, 6, 12, 12, 12, 12, 12, 12, 6, 6, 10, 10, 10, 10, 10, 6, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530043545 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000530043545 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530043545/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530043545/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530043545 Building ZINC000530043545 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530043545' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530043545 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000530043545 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530043545/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530043545 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 545) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc3c2OC(C)(C)CC3)cn1) `ZINC000530043545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530043545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530043545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000530043545 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc3c2OC(C)(C)CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 13, 13, 13, 7, 13, 13, 13, 13, 13, 13, 6, 6, 10, 10, 10, 10, 10, 6, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530043545 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530043545/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530043545 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 546) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc3c2OC(C)(C)CC3)cn1) `ZINC000530043545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530043545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530043545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000530043545 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc3c2OC(C)(C)CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 12, 12, 12, 6, 12, 12, 12, 12, 12, 12, 6, 6, 10, 10, 10, 10, 10, 6, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530043545 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000530043545 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530043545/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530043545/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530043545 Building ZINC000530047969 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047969' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047969 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000530047969 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047969/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047969 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/547 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2Cc3c(cccc3Cl)[C@@H]12) `ZINC000530047969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530047969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000530047969 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2Cc3c(cccc3Cl)[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 1, 1, 1, 1, 1, 1, 16, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 9, 9, 1, 9, 9, 1, 1, 1, 1, 10, 10, 10, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 13, 13, 13, 9, 9, 9, 9, 10, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047969 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047969/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047969 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/548 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/548' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2Cc3c(cccc3Cl)[C@@H]12) `ZINC000530047969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530047969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000530047969 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2Cc3c(cccc3Cl)[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 1, 1, 1, 1, 1, 1, 16, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 1, 9, 9, 1, 1, 1, 1, 11, 11, 11, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 9, 9, 9, 9, 11, 32, 32, 32, 32, 32] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 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: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047969 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000530047969 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047969/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047969/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047969 Building ZINC000530047969 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047969' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047969 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000530047969 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047969/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047969 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 547) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2Cc3c(cccc3Cl)[C@@H]12) `ZINC000530047969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530047969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000530047969 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2Cc3c(cccc3Cl)[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 1, 1, 1, 1, 1, 1, 16, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 9, 9, 1, 9, 9, 1, 1, 1, 1, 10, 10, 10, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 13, 13, 13, 9, 9, 9, 9, 10, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047969 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047969/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047969 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 548) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2Cc3c(cccc3Cl)[C@@H]12) `ZINC000530047969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530047969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000530047969 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2Cc3c(cccc3Cl)[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 1, 1, 1, 1, 1, 1, 16, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 1, 9, 9, 1, 1, 1, 1, 11, 11, 11, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 9, 9, 9, 9, 11, 32, 32, 32, 32, 32] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 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: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047969 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000530047969 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047969/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047969/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047969 Building ZINC000530047974 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047974' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047974 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000530047974 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047974/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047974 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/549 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2Cc3c(cccc3Cl)[C@@H]21) `ZINC000530047974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530047974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000530047974 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2Cc3c(cccc3Cl)[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 1, 1, 1, 1, 1, 1, 16, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 8, 8, 2, 8, 8, 1, 1, 1, 1, 10, 10, 10, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 9, 9, 9, 8, 8, 8, 8, 10, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/83235/xao-8058115.15/working/building/ZINC000530047974 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047974/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047974 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/550 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/550' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2Cc3c(cccc3Cl)[C@@H]21) `ZINC000530047974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530047974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000530047974 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2Cc3c(cccc3Cl)[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 1, 1, 1, 1, 1, 1, 16, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 1, 9, 9, 1, 1, 1, 1, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 12, 9, 9, 9, 9, 10, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 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: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047974 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000530047974 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047974/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047974/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047974 Building ZINC000530047974 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047974' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047974 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000530047974 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047974/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047974 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 549) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2Cc3c(cccc3Cl)[C@@H]21) `ZINC000530047974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530047974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000530047974 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2Cc3c(cccc3Cl)[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 1, 1, 1, 1, 1, 1, 16, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 8, 8, 2, 8, 8, 1, 1, 1, 1, 10, 10, 10, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 9, 9, 9, 8, 8, 8, 8, 10, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/83235/xao-8058115.15/working/building/ZINC000530047974 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047974/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047974 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 550) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2Cc3c(cccc3Cl)[C@@H]21) `ZINC000530047974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530047974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000530047974 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2Cc3c(cccc3Cl)[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 1, 1, 1, 1, 1, 1, 16, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 1, 9, 9, 1, 1, 1, 1, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 12, 9, 9, 9, 9, 10, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 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: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047974 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000530047974 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047974/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047974/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530047974 Building ZINC000530042812 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530042812' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530042812 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000530042812 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530042812/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530042812 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/551 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/551' -> `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)Nc1cccc2c1OC(C)(C)CC2) `ZINC000530042812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530042812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530042812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000530042812 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc2c1OC(C)(C)CC2 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.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 21, 40, 40, 40, 21, 40, 40, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530042812 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530042812/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530042812 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/552 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/552' -> `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)Nc1cccc2c1OC(C)(C)CC2) `ZINC000530042812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530042812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530042812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000530042812 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc2c1OC(C)(C)CC2 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.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 20, 40, 40, 40, 20, 40, 40, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530042812 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000530042812 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530042812/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530042812/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530042812 Building ZINC000530042812 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530042812' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530042812 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000530042812 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530042812/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530042812 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 551) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc2c1OC(C)(C)CC2) `ZINC000530042812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530042812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530042812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000530042812 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc2c1OC(C)(C)CC2 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.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 21, 40, 40, 40, 21, 40, 40, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530042812 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530042812/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530042812 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 552) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc2c1OC(C)(C)CC2) `ZINC000530042812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530042812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530042812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000530042812 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc2c1OC(C)(C)CC2 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.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 20, 40, 40, 40, 20, 40, 40, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530042812 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000530042812 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530042812/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530042812/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530042812 Building ZINC000432288889 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000432288889 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/553 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)O[C@H]1C[C@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000432288889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000432288889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000432288889 none CC(C)(C)O[C@H]1C[C@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 38, 38, 22, 38, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 38, 39, 39, 39, 39, 39, 39, 39, 39, 39, 38, 38, 22, 22, 14, 14, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 38, 38] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/554 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/554' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)O[C@H]1C[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000432288889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000432288889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000432288889 none CC(C)(C)O[C@H]1C[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 40, 40, 40, 23, 40, 14, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 40, 43, 43, 43, 43, 43, 43, 43, 43, 43, 40, 40, 23, 23, 14, 14, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 40, 40] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 179 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/555 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/555' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)O[C@H]1C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000432288889.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000432288889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000432288889 none CC(C)(C)O[C@H]1C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 38, 38, 22, 38, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 38, 39, 39, 39, 39, 39, 39, 39, 39, 39, 38, 38, 22, 22, 14, 14, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 38, 38] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/556 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/556' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)O[C@H]1C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000432288889.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000432288889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000432288889 none CC(C)(C)O[C@H]1C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 40, 40, 40, 23, 40, 14, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 40, 43, 43, 43, 43, 43, 43, 43, 43, 43, 40, 40, 23, 23, 14, 14, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 40, 40] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 179 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000432288889 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 Building ZINC000432288889 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000432288889 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 553) grep: /scratch/xiaobo/83235/xao-8058115.15/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)(C)O[C@H]1C[C@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000432288889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000432288889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000432288889 none CC(C)(C)O[C@H]1C[C@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 38, 38, 22, 38, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 38, 39, 39, 39, 39, 39, 39, 39, 39, 39, 38, 38, 22, 22, 14, 14, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 38, 38] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 554) grep: /scratch/xiaobo/83235/xao-8058115.15/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)(C)O[C@H]1C[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000432288889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000432288889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000432288889 none CC(C)(C)O[C@H]1C[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 40, 40, 40, 23, 40, 14, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 40, 43, 43, 43, 43, 43, 43, 43, 43, 43, 40, 40, 23, 23, 14, 14, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 40, 40] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 179 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 555) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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[C@H]1C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000432288889.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000432288889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000432288889 none CC(C)(C)O[C@H]1C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 38, 38, 22, 38, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 38, 39, 39, 39, 39, 39, 39, 39, 39, 39, 38, 38, 22, 22, 14, 14, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 38, 38] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 556) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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[C@H]1C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000432288889.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000432288889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000432288889 none CC(C)(C)O[C@H]1C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 40, 40, 40, 23, 40, 14, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 40, 43, 43, 43, 43, 43, 43, 43, 43, 43, 40, 40, 23, 23, 14, 14, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 40, 40] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 179 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000432288889 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 Building ZINC000432288889 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000432288889 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 553) grep: /scratch/xiaobo/83235/xao-8058115.15/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)(C)O[C@H]1C[C@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000432288889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000432288889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000432288889 none CC(C)(C)O[C@H]1C[C@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 38, 38, 22, 38, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 38, 39, 39, 39, 39, 39, 39, 39, 39, 39, 38, 38, 22, 22, 14, 14, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 38, 38] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 554) grep: /scratch/xiaobo/83235/xao-8058115.15/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)(C)O[C@H]1C[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000432288889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000432288889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000432288889 none CC(C)(C)O[C@H]1C[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 40, 40, 40, 23, 40, 14, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 40, 43, 43, 43, 43, 43, 43, 43, 43, 43, 40, 40, 23, 23, 14, 14, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 40, 40] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 179 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 555) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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[C@H]1C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000432288889.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000432288889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000432288889 none CC(C)(C)O[C@H]1C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 38, 38, 22, 38, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 38, 39, 39, 39, 39, 39, 39, 39, 39, 39, 38, 38, 22, 22, 14, 14, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 38, 38] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 556) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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[C@H]1C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000432288889.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000432288889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000432288889 none CC(C)(C)O[C@H]1C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 40, 40, 40, 23, 40, 14, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 40, 43, 43, 43, 43, 43, 43, 43, 43, 43, 40, 40, 23, 23, 14, 14, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 40, 40] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 179 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000432288889 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 Building ZINC000432288889 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000432288889 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 553) grep: /scratch/xiaobo/83235/xao-8058115.15/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)(C)O[C@H]1C[C@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000432288889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000432288889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000432288889 none CC(C)(C)O[C@H]1C[C@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 38, 38, 22, 38, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 38, 39, 39, 39, 39, 39, 39, 39, 39, 39, 38, 38, 22, 22, 14, 14, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 38, 38] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 554) grep: /scratch/xiaobo/83235/xao-8058115.15/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)(C)O[C@H]1C[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000432288889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000432288889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000432288889 none CC(C)(C)O[C@H]1C[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 40, 40, 40, 23, 40, 14, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 40, 43, 43, 43, 43, 43, 43, 43, 43, 43, 40, 40, 23, 23, 14, 14, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 40, 40] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 179 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 555) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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[C@H]1C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000432288889.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000432288889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000432288889 none CC(C)(C)O[C@H]1C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 38, 38, 22, 38, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 38, 39, 39, 39, 39, 39, 39, 39, 39, 39, 38, 38, 22, 22, 14, 14, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 38, 38] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 556) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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[C@H]1C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000432288889.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000432288889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000432288889 none CC(C)(C)O[C@H]1C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 40, 40, 40, 23, 40, 14, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 40, 43, 43, 43, 43, 43, 43, 43, 43, 43, 40, 40, 23, 23, 14, 14, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 40, 40] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 179 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000432288889 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432288889 Building ZINC000161589698 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161589698' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161589698 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000161589698 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161589698/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161589698 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/557 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C(C)(C)C)o1) `ZINC000161589698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000161589698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161589698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000161589698 none Cc1nnc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 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] 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, 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, 26, 26, 26, 13, 7, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 12, 12, 12, 26, 26, 26, 26, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 96 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161589698 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161589698/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161589698 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/558 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/558' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C(C)(C)C)o1) `ZINC000161589698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000161589698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161589698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000161589698 none Cc1nnc(CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 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] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 12, 7, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 10, 10, 10, 27, 27, 27, 27, 12, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 84 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161589698 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000161589698 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161589698/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161589698/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161589698 Building ZINC000161589698 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161589698' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161589698 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000161589698 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161589698/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161589698 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 557) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nnc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C(C)(C)C)o1) `ZINC000161589698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000161589698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161589698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000161589698 none Cc1nnc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 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] 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, 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, 26, 26, 26, 13, 7, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 12, 12, 12, 26, 26, 26, 26, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 96 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161589698 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161589698/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161589698 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 558) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nnc(CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C(C)(C)C)o1) `ZINC000161589698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000161589698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161589698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000161589698 none Cc1nnc(CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 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] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 12, 7, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 10, 10, 10, 27, 27, 27, 27, 12, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 84 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161589698 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000161589698 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161589698/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161589698/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161589698 Building ZINC000432437372 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432437372' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432437372 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000432437372 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432437372/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432437372 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/559 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Oc1cc(O)ccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000432437372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000432437372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432437372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000432437372 none CC(C)Oc1cc(O)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 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, 6, 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, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 20, 27, 6, 6, 6, 4, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 27, 27, 27, 27, 27, 27, 27, 6, 12, 6, 6, 2, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432437372 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432437372/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432437372 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/560 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/560' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Oc1cc(O)ccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000432437372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000432437372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432437372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000432437372 none CC(C)Oc1cc(O)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 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, 6, 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, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [31, 21, 31, 6, 6, 6, 4, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 31, 31, 31, 31, 31, 31, 31, 6, 12, 6, 6, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432437372 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000432437372 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432437372/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432437372/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432437372 Building ZINC000432437372 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432437372' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432437372 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000432437372 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432437372/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432437372 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 559) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Oc1cc(O)ccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000432437372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000432437372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432437372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000432437372 none CC(C)Oc1cc(O)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 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, 6, 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, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 20, 27, 6, 6, 6, 4, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 27, 27, 27, 27, 27, 27, 27, 6, 12, 6, 6, 2, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432437372 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432437372/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432437372 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 560) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/560: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Oc1cc(O)ccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000432437372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000432437372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432437372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000432437372 none CC(C)Oc1cc(O)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 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, 6, 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, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [31, 21, 31, 6, 6, 6, 4, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 31, 31, 31, 31, 31, 31, 31, 6, 12, 6, 6, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432437372 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000432437372 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432437372/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432437372/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432437372 Building ZINC000530206838 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206838' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206838 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000530206838 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206838/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206838 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/561 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C2CC2)cn1) `ZINC000530206838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530206838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000530206838 none COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 8, 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, 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: [43, 43, 43, 43, 43, 9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 14, 14, 43, 43, 43, 43, 43, 43, 43, 5, 3, 3, 3, 3, 14, 14, 14, 14, 14, 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: 105 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206838 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206838/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206838 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/562 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/562' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C2CC2)cn1) `ZINC000530206838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530206838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000530206838 none COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 8, 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, 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: [44, 44, 44, 44, 44, 9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 14, 14, 44, 44, 44, 44, 44, 44, 44, 5, 3, 3, 3, 3, 14, 14, 14, 14, 14, 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, 38, 39, 40]) total number of confs: 103 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206838 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000530206838 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206838/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206838/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206838 Building ZINC000530206838 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206838' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206838 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000530206838 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206838/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206838 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 561) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C2CC2)cn1) `ZINC000530206838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530206838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000530206838 none COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 8, 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, 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: [43, 43, 43, 43, 43, 9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 14, 14, 43, 43, 43, 43, 43, 43, 43, 5, 3, 3, 3, 3, 14, 14, 14, 14, 14, 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: 105 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206838 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206838/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206838 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 562) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C2CC2)cn1) `ZINC000530206838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530206838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000530206838 none COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 8, 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, 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: [44, 44, 44, 44, 44, 9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 14, 14, 44, 44, 44, 44, 44, 44, 44, 5, 3, 3, 3, 3, 14, 14, 14, 14, 14, 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, 38, 39, 40]) total number of confs: 103 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206838 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000530206838 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206838/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206838/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206838 Building ZINC000530206840 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206840' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206840 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000530206840 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206840/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206840 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/563 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C2CC2)cn1) `ZINC000530206840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530206840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000530206840 none COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 8, 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, 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: [44, 44, 44, 44, 44, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 16, 16, 44, 44, 44, 44, 44, 44, 44, 4, 3, 3, 3, 3, 16, 16, 16, 16, 16, 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, 38, 39, 40]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206840 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206840/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206840 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/564 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/564' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C2CC2)cn1) `ZINC000530206840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530206840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000530206840 none COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 8, 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, 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: [42, 42, 42, 42, 42, 9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 15, 15, 42, 42, 42, 42, 42, 42, 42, 5, 3, 3, 3, 3, 15, 15, 15, 15, 15, 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: 105 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206840 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000530206840 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206840/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206840/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206840 Building ZINC000530206840 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206840' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206840 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000530206840 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206840/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206840 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 563) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/563: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C2CC2)cn1) `ZINC000530206840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530206840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000530206840 none COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 8, 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, 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: [44, 44, 44, 44, 44, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 16, 16, 44, 44, 44, 44, 44, 44, 44, 4, 3, 3, 3, 3, 16, 16, 16, 16, 16, 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, 38, 39, 40]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206840 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206840/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206840 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 564) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/564: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C2CC2)cn1) `ZINC000530206840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530206840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000530206840 none COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 8, 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, 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: [42, 42, 42, 42, 42, 9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 15, 15, 42, 42, 42, 42, 42, 42, 42, 5, 3, 3, 3, 3, 15, 15, 15, 15, 15, 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: 105 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206840 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000530206840 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206840/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206840/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000530206840 Building ZINC000432854694 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432854694' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432854694 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000432854694 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432854694/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432854694 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/565 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(c2ccc3c(c2)OCO3)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000432854694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000432854694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432854694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000432854694 none O=C(NC1(c2ccc3c(c2)OCO3)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 7, 25, 25, 25, 25, 25, 25, 25, 25, 7, 7, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 6, 25, 25, 25, 25, 25, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 49 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432854694 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432854694/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432854694 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/566 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/566' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(c2ccc3c(c2)OCO3)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000432854694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000432854694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432854694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000432854694 none O=C(NC1(c2ccc3c(c2)OCO3)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 6, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 24, 24, 24, 24, 24, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 49 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432854694 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000432854694 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432854694/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432854694/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432854694 Building ZINC000432854694 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432854694' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432854694 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000432854694 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432854694/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432854694 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 565) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NC1(c2ccc3c(c2)OCO3)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000432854694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000432854694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432854694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000432854694 none O=C(NC1(c2ccc3c(c2)OCO3)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 7, 25, 25, 25, 25, 25, 25, 25, 25, 7, 7, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 6, 25, 25, 25, 25, 25, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 49 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432854694 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432854694/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432854694 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 566) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NC1(c2ccc3c(c2)OCO3)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000432854694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000432854694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432854694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000432854694 none O=C(NC1(c2ccc3c(c2)OCO3)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 6, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 24, 24, 24, 24, 24, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 49 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432854694 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000432854694 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432854694/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432854694/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432854694 Building ZINC000432839631 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432839631' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432839631 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000432839631 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432839631/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432839631 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/567 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1cccc(CN(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000432839631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000432839631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432839631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000432839631 none CN(C)c1cccc(CN(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 16, 30, 16, 16, 16, 16, 7, 4, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 16, 30, 30, 30, 30, 30, 30, 16, 16, 16, 7, 7, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 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, 45, 46, 47, 48, 49, 50]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432839631 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432839631/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432839631 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/568 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/568' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1cccc(CN(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000432839631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000432839631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432839631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000432839631 none CN(C)c1cccc(CN(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 31, 17, 17, 17, 17, 7, 3, 2, 3, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 17, 31, 31, 31, 31, 31, 31, 17, 17, 17, 7, 7, 3, 3, 3, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 17] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432839631 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000432839631 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432839631/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432839631/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432839631 Building ZINC000432839631 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432839631' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432839631 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000432839631 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432839631/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432839631 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 567) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN(C)c1cccc(CN(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000432839631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000432839631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432839631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000432839631 none CN(C)c1cccc(CN(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 16, 30, 16, 16, 16, 16, 7, 4, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 16, 30, 30, 30, 30, 30, 30, 16, 16, 16, 7, 7, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 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, 45, 46, 47, 48, 49, 50]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432839631 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432839631/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432839631 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 568) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN(C)c1cccc(CN(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000432839631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000432839631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432839631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000432839631 none CN(C)c1cccc(CN(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 31, 17, 17, 17, 17, 7, 3, 2, 3, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 17, 31, 31, 31, 31, 31, 31, 17, 17, 17, 7, 7, 3, 3, 3, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 17] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432839631 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000432839631 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432839631/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432839631/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432839631 Building ZINC000175737682 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737682' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737682 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175737682 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737682/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737682 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/569 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000175737682.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175737682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000175737682 none C[C@@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 14, 14, 41, 41, 50, 50, 50, 50, 2, 5, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 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, 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/83235/xao-8058115.15/working/building/ZINC000175737682 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737682/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737682 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/570 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/570' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000175737682.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175737682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000175737682 none C[C@@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 14, 14, 40, 40, 50, 50, 50, 50, 2, 5, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/83235/xao-8058115.15/working/building/ZINC000175737682 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175737682 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737682/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737682/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737682 Building ZINC000175737682 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737682' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737682 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175737682 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737682/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737682 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 569) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000175737682.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175737682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000175737682 none C[C@@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 14, 14, 41, 41, 50, 50, 50, 50, 2, 5, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 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, 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/83235/xao-8058115.15/working/building/ZINC000175737682 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737682/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737682 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 570) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000175737682.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175737682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000175737682 none C[C@@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 14, 14, 40, 40, 50, 50, 50, 50, 2, 5, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/83235/xao-8058115.15/working/building/ZINC000175737682 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175737682 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737682/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737682/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737682 Building ZINC000175737703 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737703' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737703 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175737703 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737703/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737703 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/571 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000175737703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175737703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000175737703 none C[C@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 14, 14, 40, 40, 50, 50, 50, 50, 2, 5, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 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, 40, 41]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737703 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737703/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737703 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/572 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/572' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000175737703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175737703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000175737703 none C[C@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 14, 14, 42, 42, 50, 50, 50, 50, 2, 5, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 3, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 3, 3, 3, 3] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737703 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175737703 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737703/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737703/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737703 Building ZINC000175737703 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737703' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737703 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175737703 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737703/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737703 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 571) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000175737703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175737703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000175737703 none C[C@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 14, 14, 40, 40, 50, 50, 50, 50, 2, 5, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 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, 40, 41]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737703 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737703/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737703 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 572) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000175737703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175737703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000175737703 none C[C@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 14, 14, 42, 42, 50, 50, 50, 50, 2, 5, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 3, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 3, 3, 3, 3] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737703 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175737703 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737703/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737703/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175737703 Building ZINC000432955261 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432955261' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432955261 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000432955261 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432955261/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432955261 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/573 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CC1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CCCC1) `ZINC000432955261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000432955261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432955261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000432955261 none CCOC(=O)CC1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 29, 46, 10, 6, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 10, 50, 50, 50, 50, 50, 29, 29, 4, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432955261 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432955261/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432955261 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/574 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/574' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CC1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CCCC1) `ZINC000432955261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000432955261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432955261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000432955261 none CCOC(=O)CC1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 47, 27, 47, 10, 6, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 10, 50, 50, 50, 50, 50, 27, 27, 4, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432955261 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000432955261 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432955261/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432955261/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432955261 Building ZINC000432955261 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432955261' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432955261 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000432955261 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432955261/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432955261 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 573) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCOC(=O)CC1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CCCC1) `ZINC000432955261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000432955261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432955261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000432955261 none CCOC(=O)CC1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 29, 46, 10, 6, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 10, 50, 50, 50, 50, 50, 29, 29, 4, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432955261 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432955261/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432955261 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 574) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCOC(=O)CC1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CCCC1) `ZINC000432955261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000432955261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432955261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000432955261 none CCOC(=O)CC1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 47, 27, 47, 10, 6, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 10, 50, 50, 50, 50, 50, 27, 27, 4, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432955261 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000432955261 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432955261/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432955261/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000432955261 Building ZINC000161889256 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889256' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889256 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000161889256 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889256/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889256 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/575 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/575' -> `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)[C@H](O)c1ccc(F)cc1) `ZINC000161889256.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000161889256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000161889256 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](O)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 4, 15, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 25, 25, 25, 26, 26, 25, 25, 26, 26, 15, 15, 15, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 75, 26, 26, 26, 26] 150 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889256 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889256/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889256 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/576 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/576' -> `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)[C@H](O)c1ccc(F)cc1) `ZINC000161889256.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000161889256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000161889256 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](O)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 4, 14, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 14, 25, 25, 25, 26, 26, 25, 25, 26, 26, 14, 14, 14, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 75, 26, 26, 26, 26] 150 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889256 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000161889256 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889256/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889256/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889256 Building ZINC000161889256 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889256' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889256 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000161889256 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889256/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889256 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 575) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](O)c1ccc(F)cc1) `ZINC000161889256.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000161889256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000161889256 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](O)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 4, 15, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 25, 25, 25, 26, 26, 25, 25, 26, 26, 15, 15, 15, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 75, 26, 26, 26, 26] 150 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889256 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889256/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889256 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 576) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](O)c1ccc(F)cc1) `ZINC000161889256.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000161889256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000161889256 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](O)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 4, 14, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 14, 25, 25, 25, 26, 26, 25, 25, 26, 26, 14, 14, 14, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 75, 26, 26, 26, 26] 150 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889256 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000161889256 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889256/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889256/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889256 Building ZINC000161889417 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889417' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889417 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000161889417 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889417/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889417 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/577 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/577' -> `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)[C@H](O)c1ccc(F)cc1) `ZINC000161889417.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000161889417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000161889417 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](O)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 12, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 12, 12, 12, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 66, 22, 22, 22, 22] 150 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]) total number of confs: 158 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889417 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889417/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889417 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/578 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/578' -> `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)[C@H](O)c1ccc(F)cc1) `ZINC000161889417.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000161889417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889417/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000161889417 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](O)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 11, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 11, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 81, 27, 27, 27, 27] 150 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]) total number of confs: 195 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889417 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000161889417 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889417/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889417/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889417 Building ZINC000161889417 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889417' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889417 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000161889417 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889417/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889417 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 577) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](O)c1ccc(F)cc1) `ZINC000161889417.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000161889417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000161889417 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](O)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 12, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 12, 12, 12, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 66, 22, 22, 22, 22] 150 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]) total number of confs: 158 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889417 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889417/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889417 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 578) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](O)c1ccc(F)cc1) `ZINC000161889417.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000161889417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889417/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000161889417 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](O)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 11, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 11, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 81, 27, 27, 27, 27] 150 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]) total number of confs: 195 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889417 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000161889417 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889417/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889417/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889417 Building ZINC000161889555 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889555' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889555 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000161889555 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889555/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889555 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/579 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/579' -> `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)[C@@H](O)c1ccc(F)cc1) `ZINC000161889555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000161889555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000161889555 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](O)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 11, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 11, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 81, 27, 27, 27, 27] 150 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]) total number of confs: 195 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889555 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889555/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889555 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/580 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/580' -> `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)[C@@H](O)c1ccc(F)cc1) `ZINC000161889555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000161889555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000161889555 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](O)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 12, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 12, 12, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 69, 23, 23, 23, 23] 150 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]) total number of confs: 164 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889555 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000161889555 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889555/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889555/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889555 Building ZINC000161889555 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889555' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889555 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000161889555 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889555/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889555 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 579) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](O)c1ccc(F)cc1) `ZINC000161889555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000161889555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000161889555 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](O)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 11, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 11, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 81, 27, 27, 27, 27] 150 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]) total number of confs: 195 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889555 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889555/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889555 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 580) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](O)c1ccc(F)cc1) `ZINC000161889555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000161889555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000161889555 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](O)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 12, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 12, 12, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 69, 23, 23, 23, 23] 150 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]) total number of confs: 164 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889555 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000161889555 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889555/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889555/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889555 Building ZINC000161889692 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889692' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889692 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000161889692 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889692/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889692 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/581 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/581' -> `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)[C@@H](O)c1ccc(F)cc1) `ZINC000161889692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000161889692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000161889692 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](O)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 4, 13, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 13, 25, 25, 25, 26, 26, 26, 26, 26, 26, 13, 13, 13, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 75, 26, 26, 26, 26] 150 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889692 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889692/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889692 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/582 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/582' -> `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)[C@@H](O)c1ccc(F)cc1) `ZINC000161889692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000161889692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000161889692 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](O)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 4, 15, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 25, 25, 25, 26, 26, 26, 26, 26, 26, 15, 15, 15, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 75, 26, 26, 26, 26] 150 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]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889692 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000161889692 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889692/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889692/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889692 Building ZINC000161889692 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889692' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889692 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000161889692 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889692/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889692 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 581) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](O)c1ccc(F)cc1) `ZINC000161889692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000161889692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000161889692 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](O)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 4, 13, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 13, 25, 25, 25, 26, 26, 26, 26, 26, 26, 13, 13, 13, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 75, 26, 26, 26, 26] 150 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889692 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889692/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889692 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 582) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](O)c1ccc(F)cc1) `ZINC000161889692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000161889692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000161889692 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](O)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 4, 15, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 25, 25, 25, 26, 26, 26, 26, 26, 26, 15, 15, 15, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 75, 26, 26, 26, 26] 150 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]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889692 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000161889692 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889692/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889692/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000161889692 Building ZINC000760872473 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760872473' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760872473 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760872473 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760872473/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760872473 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/583 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(Cl)n1) `ZINC000760872473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760872473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760872473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000760872473 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(Cl)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 16, 8, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 16, 16, 16, 16, 5, 5, 1, 5, 1, 1, 1, 12, 12, 12, 12, 24, 24, 24, 12, 16, 16, 16, 17, 17, 17, 16, 16, 5, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760872473 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760872473/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760872473 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/584 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/584' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(Cl)n1) `ZINC000760872473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760872473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760872473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000760872473 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(Cl)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 16, 8, 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, 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] 0 hydrogens 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, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 25, 25, 25, 11, 16, 16, 16, 16, 16, 16, 16, 16, 5, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760872473 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000760872473 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760872473/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760872473/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760872473 Building ZINC000760872473 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760872473' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760872473 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760872473 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760872473/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760872473 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 583) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(Cl)n1) `ZINC000760872473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760872473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760872473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000760872473 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(Cl)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 16, 8, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 16, 16, 16, 16, 5, 5, 1, 5, 1, 1, 1, 12, 12, 12, 12, 24, 24, 24, 12, 16, 16, 16, 17, 17, 17, 16, 16, 5, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760872473 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760872473/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760872473 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 584) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(Cl)n1) `ZINC000760872473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760872473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760872473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000760872473 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(Cl)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 16, 8, 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, 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] 0 hydrogens 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, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 25, 25, 25, 11, 16, 16, 16, 16, 16, 16, 16, 16, 5, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760872473 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000760872473 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760872473/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760872473/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000760872473 Building ZINC000433539933 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433539933' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433539933 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000433539933 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433539933/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433539933 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/585 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cccc(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000433539933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000433539933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433539933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000433539933 none CCOc1cccc(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 17, 17, 17, 17, 17, 11, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 17, 37, 37, 37, 37, 37, 17, 17, 17, 11, 11, 8, 8, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 17] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433539933 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433539933/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433539933 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/586 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/586' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cccc(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000433539933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000433539933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433539933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000433539933 none CCOc1cccc(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 12, 9, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 17, 35, 35, 35, 35, 35, 17, 17, 17, 12, 12, 9, 9, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 17] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433539933 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000433539933 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433539933/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433539933/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433539933 Building ZINC000433539933 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433539933' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433539933 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000433539933 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433539933/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433539933 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 585) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCOc1cccc(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000433539933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000433539933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433539933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000433539933 none CCOc1cccc(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 17, 17, 17, 17, 17, 11, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 17, 37, 37, 37, 37, 37, 17, 17, 17, 11, 11, 8, 8, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 17] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433539933 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433539933/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433539933 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 586) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCOc1cccc(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000433539933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000433539933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433539933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000433539933 none CCOc1cccc(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 12, 9, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 17, 35, 35, 35, 35, 35, 17, 17, 17, 12, 12, 9, 9, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 17] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433539933 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000433539933 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433539933/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433539933/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433539933 Building ZINC000433544840 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433544840' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433544840 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000433544840 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433544840/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433544840 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/587 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCc3ccc(F)cc3C2)cn1) `ZINC000433544840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000433544840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433544840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000433544840 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCc3ccc(F)cc3C2)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', '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, 5, 1, 1, 1, 1, 15, 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] 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: [14, 6, 14, 14, 6, 6, 1, 1, 1, 2, 6, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433544840 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433544840/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433544840 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/588 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/588' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCc3ccc(F)cc3C2)cn1) `ZINC000433544840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000433544840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433544840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000433544840 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCc3ccc(F)cc3C2)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', '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, 5, 1, 1, 1, 1, 15, 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] 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: [12, 6, 12, 12, 6, 6, 1, 1, 1, 2, 7, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433544840 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000433544840 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433544840/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433544840/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433544840 Building ZINC000433544840 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433544840' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433544840 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000433544840 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433544840/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433544840 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 587) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCc3ccc(F)cc3C2)cn1) `ZINC000433544840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000433544840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433544840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000433544840 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCc3ccc(F)cc3C2)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', '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, 5, 1, 1, 1, 1, 15, 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] 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: [14, 6, 14, 14, 6, 6, 1, 1, 1, 2, 6, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433544840 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433544840/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433544840 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 588) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCc3ccc(F)cc3C2)cn1) `ZINC000433544840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000433544840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433544840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000433544840 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCc3ccc(F)cc3C2)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', '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, 5, 1, 1, 1, 1, 15, 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] 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: [12, 6, 12, 12, 6, 6, 1, 1, 1, 2, 7, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433544840 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000433544840 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433544840/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433544840/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433544840 Building ZINC000433738240 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738240' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738240 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000433738240 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738240/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738240 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/589 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](CC(F)(F)F)C2)cn1) `ZINC000433738240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000433738240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000433738240 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](CC(F)(F)F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 15, 15, 15, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 12, 12, 5, 5, 1, 1, 1, 1, 2, 3, 10, 10, 10, 10, 10, 20, 20, 20, 20, 10, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 10, 10, 10, 10, 20, 20, 10, 10, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738240 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738240/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738240 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/590 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/590' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](CC(F)(F)F)C2)cn1) `ZINC000433738240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000433738240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000433738240 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](CC(F)(F)F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 15, 15, 15, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 2, 3, 8, 8, 8, 8, 8, 17, 17, 17, 17, 8, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 8, 8, 8, 8, 17, 17, 8, 8, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738240 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000433738240 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738240/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738240/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738240 Building ZINC000433738240 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738240' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738240 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000433738240 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738240/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738240 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 589) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](CC(F)(F)F)C2)cn1) `ZINC000433738240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000433738240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000433738240 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](CC(F)(F)F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 15, 15, 15, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 12, 12, 5, 5, 1, 1, 1, 1, 2, 3, 10, 10, 10, 10, 10, 20, 20, 20, 20, 10, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 10, 10, 10, 10, 20, 20, 10, 10, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738240 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738240/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738240 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 590) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](CC(F)(F)F)C2)cn1) `ZINC000433738240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000433738240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000433738240 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](CC(F)(F)F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 15, 15, 15, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 2, 3, 8, 8, 8, 8, 8, 17, 17, 17, 17, 8, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 8, 8, 8, 8, 17, 17, 8, 8, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738240 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000433738240 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738240/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738240/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738240 Building ZINC000433738242 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738242' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738242 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000433738242 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738242/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738242 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/591 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](CC(F)(F)F)C2)cn1) `ZINC000433738242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000433738242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000433738242 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](CC(F)(F)F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 15, 15, 15, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 2, 3, 8, 8, 8, 8, 8, 17, 17, 17, 17, 8, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 8, 8, 8, 8, 17, 17, 8, 8, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738242 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738242/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738242 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/592 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/592' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](CC(F)(F)F)C2)cn1) `ZINC000433738242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000433738242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000433738242 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](CC(F)(F)F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 15, 15, 15, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 12, 12, 5, 5, 1, 1, 1, 1, 2, 3, 10, 10, 10, 10, 10, 20, 20, 20, 20, 10, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 10, 10, 10, 10, 20, 20, 10, 10, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738242 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000433738242 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738242/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738242/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738242 Building ZINC000433738242 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738242' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738242 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000433738242 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738242/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738242 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 591) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](CC(F)(F)F)C2)cn1) `ZINC000433738242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000433738242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000433738242 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](CC(F)(F)F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 15, 15, 15, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 2, 3, 8, 8, 8, 8, 8, 17, 17, 17, 17, 8, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 8, 8, 8, 8, 17, 17, 8, 8, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738242 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738242/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738242 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 592) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](CC(F)(F)F)C2)cn1) `ZINC000433738242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000433738242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000433738242 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](CC(F)(F)F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 15, 15, 15, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 12, 12, 5, 5, 1, 1, 1, 1, 2, 3, 10, 10, 10, 10, 10, 20, 20, 20, 20, 10, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 10, 10, 10, 10, 20, 20, 10, 10, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738242 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000433738242 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738242/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738242/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433738242 Building ZINC000175755373 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755373' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755373 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175755373 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755373/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755373 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/593 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000175755373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175755373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000175755373 none C[C@@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 12, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 26, 26, 31, 31, 31, 31, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755373 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755373/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755373 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/594 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/594' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000175755373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175755373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000175755373 none C[C@@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 12, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 25, 25, 29, 29, 29, 29, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755373 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175755373 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755373/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755373/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755373 Building ZINC000175755373 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755373' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755373 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175755373 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755373/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755373 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 593) grep: /scratch/xiaobo/83235/xao-8058115.15/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](C(=O)OC(C)(C)C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000175755373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175755373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000175755373 none C[C@@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 12, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 26, 26, 31, 31, 31, 31, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755373 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755373/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755373 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 594) grep: /scratch/xiaobo/83235/xao-8058115.15/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](C(=O)OC(C)(C)C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000175755373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175755373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000175755373 none C[C@@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 12, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 25, 25, 29, 29, 29, 29, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755373 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175755373 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755373/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755373/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755373 Building ZINC000175755394 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755394' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175755394 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755394/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/595 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000175755394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175755394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000175755394 none C[C@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 12, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 24, 24, 28, 28, 28, 28, 2, 4, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755394/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/596 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/596' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000175755394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175755394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000175755394 none C[C@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 12, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 27, 27, 31, 32, 32, 32, 2, 4, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175755394 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755394/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755394/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755394 Building ZINC000175755394 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755394' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175755394 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755394/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 595) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/595: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000175755394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175755394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000175755394 none C[C@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 12, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 24, 24, 28, 28, 28, 28, 2, 4, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755394/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 596) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/596: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000175755394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175755394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000175755394 none C[C@H](C(=O)OC(C)(C)C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 12, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 27, 27, 31, 32, 32, 32, 2, 4, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175755394 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755394/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755394/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175755394 Building ZINC000433920948 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920948' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920948 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000433920948 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920948/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920948 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/597 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1cccc(O)c1)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000433920948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000433920948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000433920948 none C[C@H](c1cccc(O)c1)N(C)C(=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', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 10, 10, 29, 29, 29, 29, 29, 29, 2, 4, 1, 2, 1, 1, 1, 3, 3, 3, 3, 5, 5, 5, 3, 10, 10, 10, 29, 29, 29, 58, 29, 4, 4, 4, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920948 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920948/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920948 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/598 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/598' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1cccc(O)c1)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000433920948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000433920948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000433920948 none C[C@H](c1cccc(O)c1)N(C)C(=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', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 3, 9, 9, 25, 25, 25, 25, 25, 25, 2, 3, 1, 2, 1, 1, 1, 5, 5, 5, 5, 10, 10, 10, 5, 9, 9, 9, 25, 25, 25, 50, 25, 3, 3, 3, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920948 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000433920948 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920948/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920948/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920948 Building ZINC000433920948 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920948' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920948 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000433920948 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920948/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920948 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 597) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H](c1cccc(O)c1)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000433920948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000433920948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000433920948 none C[C@H](c1cccc(O)c1)N(C)C(=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', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 10, 10, 29, 29, 29, 29, 29, 29, 2, 4, 1, 2, 1, 1, 1, 3, 3, 3, 3, 5, 5, 5, 3, 10, 10, 10, 29, 29, 29, 58, 29, 4, 4, 4, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920948 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920948/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920948 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 598) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H](c1cccc(O)c1)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000433920948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000433920948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000433920948 none C[C@H](c1cccc(O)c1)N(C)C(=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', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 3, 9, 9, 25, 25, 25, 25, 25, 25, 2, 3, 1, 2, 1, 1, 1, 5, 5, 5, 5, 10, 10, 10, 5, 9, 9, 9, 25, 25, 25, 50, 25, 3, 3, 3, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920948 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000433920948 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920948/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920948/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920948 Building ZINC000433920951 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920951' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920951 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000433920951 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920951/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920951 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/599 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](c1cccc(O)c1)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000433920951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000433920951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000433920951 none C[C@@H](c1cccc(O)c1)N(C)C(=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', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 10, 10, 28, 28, 28, 28, 28, 28, 2, 3, 1, 2, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 10, 10, 10, 28, 28, 28, 56, 28, 3, 3, 3, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920951 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920951/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920951 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/600 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/600' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](c1cccc(O)c1)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000433920951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000433920951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000433920951 none C[C@@H](c1cccc(O)c1)N(C)C(=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', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 10, 10, 30, 30, 30, 30, 30, 30, 2, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 4, 4, 4, 2, 10, 10, 10, 30, 30, 30, 60, 30, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920951 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000433920951 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920951/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920951/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920951 Building ZINC000433920951 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920951' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920951 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000433920951 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920951/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920951 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 599) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H](c1cccc(O)c1)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000433920951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000433920951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000433920951 none C[C@@H](c1cccc(O)c1)N(C)C(=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', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 10, 10, 28, 28, 28, 28, 28, 28, 2, 3, 1, 2, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 10, 10, 10, 28, 28, 28, 56, 28, 3, 3, 3, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920951 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920951/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920951 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 600) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H](c1cccc(O)c1)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000433920951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000433920951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000433920951 none C[C@@H](c1cccc(O)c1)N(C)C(=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', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 10, 10, 30, 30, 30, 30, 30, 30, 2, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 4, 4, 4, 2, 10, 10, 10, 30, 30, 30, 60, 30, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920951 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000433920951 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920951/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920951/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433920951 Building ZINC000532083906 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000532083906' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000532083906 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000532083906 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000532083906/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000532083906 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/601 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C)CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000532083906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000532083906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000532083906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000532083906 none COC(C)(C)CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 43, 43, 9, 4, 9, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 43, 43, 43, 43, 43, 43, 19, 19, 9, 9, 9, 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, 33, 34, 35, 36]) total number of confs: 194 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000532083906 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000532083906/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000532083906 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/602 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/602' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C)CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000532083906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000532083906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000532083906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000532083906 none COC(C)(C)CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 43, 43, 9, 4, 9, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 43, 43, 43, 43, 43, 43, 19, 19, 9, 9, 9, 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, 33, 34, 35, 36]) total number of confs: 194 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000532083906 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000532083906 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000532083906/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000532083906/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000532083906 Building ZINC000532083906 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000532083906' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000532083906 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000532083906 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000532083906/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000532083906 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 601) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC(C)(C)CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000532083906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000532083906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000532083906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000532083906 none COC(C)(C)CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 43, 43, 9, 4, 9, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 43, 43, 43, 43, 43, 43, 19, 19, 9, 9, 9, 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, 33, 34, 35, 36]) total number of confs: 194 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000532083906 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000532083906/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000532083906 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 602) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC(C)(C)CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000532083906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000532083906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000532083906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000532083906 none COC(C)(C)CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 43, 43, 9, 4, 9, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 43, 43, 43, 43, 43, 43, 19, 19, 9, 9, 9, 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, 33, 34, 35, 36]) total number of confs: 194 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000532083906 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000532083906 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000532083906/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000532083906/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000532083906 Building ZINC000433994763 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433994763' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433994763 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000433994763 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433994763/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433994763 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/603 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(F)cc(F)c1)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000433994763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000433994763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433994763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000433994763 none CN(Cc1cc(F)cc(F)c1)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 15, 1, 1, 15, 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] 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] 0 hydrogens need 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, 18, 24, 24, 24, 24, 24, 24, 24, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 5, 5, 5, 18, 18, 24, 24, 24, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433994763 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433994763/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433994763 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/604 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/604' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(F)cc(F)c1)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000433994763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000433994763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433994763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000433994763 none CN(Cc1cc(F)cc(F)c1)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 15, 1, 1, 15, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 17, 23, 23, 23, 22, 23, 23, 23, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 5, 5, 5, 17, 17, 23, 23, 23, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433994763 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000433994763 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433994763/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433994763/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433994763 Building ZINC000433994763 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433994763' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433994763 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000433994763 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433994763/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433994763 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 603) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN(Cc1cc(F)cc(F)c1)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000433994763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000433994763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433994763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000433994763 none CN(Cc1cc(F)cc(F)c1)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 15, 1, 1, 15, 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] 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] 0 hydrogens need 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, 18, 24, 24, 24, 24, 24, 24, 24, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 5, 5, 5, 18, 18, 24, 24, 24, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433994763 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433994763/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433994763 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 604) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN(Cc1cc(F)cc(F)c1)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000433994763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000433994763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433994763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000433994763 none CN(Cc1cc(F)cc(F)c1)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 15, 1, 1, 15, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 17, 23, 23, 23, 22, 23, 23, 23, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 5, 5, 5, 17, 17, 23, 23, 23, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433994763 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000433994763 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433994763/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433994763/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000433994763 Building ZINC000434185195 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185195' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185195 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000434185195 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185195/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185195 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/605 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1) `ZINC000434185195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000434185195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000434185195 none CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 16, 20, 10, 16, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 16, 28, 28, 28, 28, 28, 20, 20, 20, 20, 20, 20, 20, 10, 10, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 28, 28, 28, 28] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 149 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185195 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185195/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185195 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/606 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/606' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1) `ZINC000434185195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000434185195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000434185195 none CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 18, 12, 17, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 17, 32, 32, 32, 32, 32, 18, 18, 18, 18, 18, 18, 18, 12, 12, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 32, 32, 32, 32] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 143 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185195 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000434185195 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185195/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185195/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185195 Building ZINC000434185195 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185195' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185195 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000434185195 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185195/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185195 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 605) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1) `ZINC000434185195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000434185195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000434185195 none CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 16, 20, 10, 16, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 16, 28, 28, 28, 28, 28, 20, 20, 20, 20, 20, 20, 20, 10, 10, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 28, 28, 28, 28] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 149 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185195 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185195/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185195 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 606) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1) `ZINC000434185195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000434185195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000434185195 none CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 18, 12, 17, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 17, 32, 32, 32, 32, 32, 18, 18, 18, 18, 18, 18, 18, 12, 12, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 32, 32, 32, 32] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 143 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185195 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000434185195 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185195/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185195/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185195 Building ZINC000434185196 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185196' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185196 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000434185196 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185196/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185196 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/607 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1) `ZINC000434185196.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000434185196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000434185196 none CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 17, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 17, 31, 31, 31, 31, 31, 17, 17, 17, 17, 17, 17, 17, 11, 11, 2, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 31, 31, 31, 31] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 132 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185196 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185196/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185196 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/608 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/608' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1) `ZINC000434185196.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000434185196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000434185196 none CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 15, 18, 9, 15, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 15, 27, 27, 27, 27, 27, 18, 18, 18, 18, 18, 18, 18, 9, 9, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 143 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185196 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000434185196 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185196/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185196/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185196 Building ZINC000434185196 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185196' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185196 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000434185196 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185196/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185196 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 607) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1) `ZINC000434185196.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000434185196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000434185196 none CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 17, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 17, 31, 31, 31, 31, 31, 17, 17, 17, 17, 17, 17, 17, 11, 11, 2, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 31, 31, 31, 31] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 132 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185196 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185196/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185196 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 608) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1) `ZINC000434185196.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000434185196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000434185196 none CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 15, 18, 9, 15, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 15, 27, 27, 27, 27, 27, 18, 18, 18, 18, 18, 18, 18, 9, 9, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 143 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185196 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000434185196 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185196/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185196/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434185196 Building ZINC000434313513 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434313513' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434313513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000434313513 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434313513/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434313513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/609 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)n(C2CCOCC2)n1) `ZINC000434313513.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000434313513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434313513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000434313513 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)n(C2CCOCC2)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', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 5, 5, 5, 12, 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, 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: [18, 18, 18, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 18, 27, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 8, 3, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 138 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434313513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434313513/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434313513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/610 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/610' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)n(C2CCOCC2)n1) `ZINC000434313513.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000434313513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434313513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000434313513 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)n(C2CCOCC2)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', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 5, 5, 5, 12, 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, 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: [18, 18, 18, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 18, 27, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 8, 3, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434313513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000434313513 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434313513/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434313513/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434313513 Building ZINC000434313513 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434313513' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434313513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000434313513 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434313513/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434313513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 609) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)n(C2CCOCC2)n1) `ZINC000434313513.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000434313513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434313513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000434313513 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)n(C2CCOCC2)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', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 5, 5, 5, 12, 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, 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: [18, 18, 18, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 18, 27, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 8, 3, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 138 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434313513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434313513/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434313513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 610) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)n(C2CCOCC2)n1) `ZINC000434313513.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000434313513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434313513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000434313513 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)n(C2CCOCC2)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', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 5, 5, 5, 12, 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, 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: [18, 18, 18, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 18, 27, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 8, 3, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434313513 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000434313513 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434313513/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434313513/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000434313513 Building ZINC000435275906 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275906' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275906 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000435275906 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275906/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275906 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/611 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc([C@@H]2CNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000435275906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000435275906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000435275906 none O=C(Nc1cccc([C@@H]2CNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 7, 7, 6, 7, 13, 27, 27, 27, 27, 27, 27, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 6, 27, 27, 27, 27, 27, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275906 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275906/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275906 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/612 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/612' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc([C@@H]2CNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000435275906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000435275906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000435275906 none O=C(Nc1cccc([C@@H]2CNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 7, 7, 2, 7, 13, 28, 28, 28, 28, 28, 28, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 2, 28, 28, 28, 28, 28, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275906 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000435275906 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275906/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275906/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275906 Building ZINC000435275906 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275906' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275906 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000435275906 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275906/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275906 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 611) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(Nc1cccc([C@@H]2CNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000435275906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000435275906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000435275906 none O=C(Nc1cccc([C@@H]2CNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 7, 7, 6, 7, 13, 27, 27, 27, 27, 27, 27, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 6, 27, 27, 27, 27, 27, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275906 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275906/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275906 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 612) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(Nc1cccc([C@@H]2CNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000435275906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000435275906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000435275906 none O=C(Nc1cccc([C@@H]2CNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 7, 7, 2, 7, 13, 28, 28, 28, 28, 28, 28, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 2, 28, 28, 28, 28, 28, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275906 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000435275906 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275906/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275906/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275906 Building ZINC000435275907 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275907' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275907 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000435275907 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275907/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275907 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/613 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc([C@H]2CNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000435275907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000435275907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000435275907 none O=C(Nc1cccc([C@H]2CNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 7, 7, 7, 7, 13, 26, 26, 26, 26, 26, 26, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 7, 26, 26, 26, 26, 26, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275907 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275907/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275907 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/614 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/614' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc([C@H]2CNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000435275907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000435275907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000435275907 none O=C(Nc1cccc([C@H]2CNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 3, 8, 14, 28, 28, 28, 28, 28, 28, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 7, 28, 28, 28, 28, 28, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275907 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000435275907 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275907/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275907/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275907 Building ZINC000435275907 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275907' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275907 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000435275907 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275907/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275907 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 613) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(Nc1cccc([C@H]2CNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000435275907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000435275907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000435275907 none O=C(Nc1cccc([C@H]2CNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 7, 7, 7, 7, 13, 26, 26, 26, 26, 26, 26, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 7, 26, 26, 26, 26, 26, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275907 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275907/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275907 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 614) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(Nc1cccc([C@H]2CNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000435275907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000435275907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000435275907 none O=C(Nc1cccc([C@H]2CNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 3, 8, 14, 28, 28, 28, 28, 28, 28, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 7, 28, 28, 28, 28, 28, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275907 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000435275907 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275907/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275907/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435275907 Building ZINC000435281989 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281989' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281989 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000435281989 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281989/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281989 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/615 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc([C@H]2CNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000435281989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000435281989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000435281989 none O=C(Nc1cccc([C@H]2CNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [3, 1, 3, 3, 12, 12, 3, 12, 21, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 12, 12, 5, 50, 50, 50, 50, 50, 12, 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281989 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281989/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281989 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/616 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/616' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc([C@H]2CNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000435281989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000435281989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000435281989 none O=C(Nc1cccc([C@H]2CNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [3, 1, 3, 3, 11, 11, 11, 11, 20, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 11, 11, 11, 50, 50, 50, 50, 50, 11, 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281989 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000435281989 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281989/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281989/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281989 Building ZINC000435281989 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281989' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281989 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000435281989 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281989/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281989 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 615) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(Nc1cccc([C@H]2CNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000435281989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000435281989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000435281989 none O=C(Nc1cccc([C@H]2CNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [3, 1, 3, 3, 12, 12, 3, 12, 21, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 12, 12, 5, 50, 50, 50, 50, 50, 12, 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281989 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281989/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281989 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 616) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(Nc1cccc([C@H]2CNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000435281989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000435281989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000435281989 none O=C(Nc1cccc([C@H]2CNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [3, 1, 3, 3, 11, 11, 11, 11, 20, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 11, 11, 11, 50, 50, 50, 50, 50, 11, 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281989 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000435281989 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281989/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281989/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281989 Building ZINC000435281990 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281990' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281990 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000435281990 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281990/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281990 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/617 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc([C@@H]2CNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000435281990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000435281990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000435281990 none O=C(Nc1cccc([C@@H]2CNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [3, 1, 3, 3, 11, 11, 5, 11, 20, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 11, 11, 5, 50, 50, 50, 50, 50, 11, 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281990 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281990/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281990 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/618 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/618' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc([C@@H]2CNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000435281990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000435281990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000435281990 none O=C(Nc1cccc([C@@H]2CNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [3, 1, 3, 3, 12, 12, 3, 12, 21, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 12, 12, 3, 50, 50, 50, 50, 50, 12, 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281990 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000435281990 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281990/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281990/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281990 Building ZINC000435281990 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281990' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281990 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000435281990 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281990/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281990 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 617) grep: /scratch/xiaobo/83235/xao-8058115.15/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(Nc1cccc([C@@H]2CNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000435281990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000435281990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000435281990 none O=C(Nc1cccc([C@@H]2CNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [3, 1, 3, 3, 11, 11, 5, 11, 20, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 11, 11, 5, 50, 50, 50, 50, 50, 11, 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281990 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281990/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281990 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 618) grep: /scratch/xiaobo/83235/xao-8058115.15/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(Nc1cccc([C@@H]2CNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000435281990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000435281990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000435281990 none O=C(Nc1cccc([C@@H]2CNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [3, 1, 3, 3, 12, 12, 3, 12, 21, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 12, 12, 3, 50, 50, 50, 50, 50, 12, 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281990 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000435281990 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281990/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281990/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435281990 Building ZINC000534010664 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000534010664' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000534010664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534010664 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000534010664/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000534010664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/619 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)c1nc2ccccc2s1) `ZINC000534010664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534010664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000534010664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000534010664 none CCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)c1nc2ccccc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 15, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6, 5, 15, 15, 15, 15, 15, 5, 14, 14, 14, 14] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000534010664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000534010664/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000534010664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/620 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/620' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)c1nc2ccccc2s1) `ZINC000534010664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534010664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000534010664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000534010664 none CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)c1nc2ccccc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 17, 5, 4, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 5, 15, 15, 15, 15] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000534010664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000534010664 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000534010664/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000534010664/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000534010664 Building ZINC000534010664 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000534010664' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000534010664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534010664 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000534010664/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000534010664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 619) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)c1nc2ccccc2s1) `ZINC000534010664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534010664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000534010664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000534010664 none CCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)c1nc2ccccc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 15, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6, 5, 15, 15, 15, 15, 15, 5, 14, 14, 14, 14] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000534010664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000534010664/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000534010664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 620) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)c1nc2ccccc2s1) `ZINC000534010664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534010664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000534010664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000534010664 none CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)c1nc2ccccc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 17, 5, 4, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 5, 15, 15, 15, 15] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000534010664 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000534010664 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000534010664/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000534010664/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000534010664 Building ZINC000435752319 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000435752319 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/621 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CCCN1C1CCCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752319.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000435752319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752319 none O=C(NC[C@@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 23, 37, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 22, 22, 37, 37, 37, 37, 37, 37, 50, 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, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/622 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/622' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CCCN1C1CCCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752319.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000435752319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752319 none O=C(NC[C@@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 33, 33, 33, 33, 33, 49, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 33, 33, 33, 33, 33, 33, 50, 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, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/623 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/623' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CCCN1C1CCCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752319.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000435752319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752319 none O=C(NC[C@@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 23, 37, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 22, 22, 37, 37, 37, 37, 37, 37, 50, 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, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/624 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/624' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CCCN1C1CCCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752319.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000435752319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752319 none O=C(NC[C@@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 33, 33, 33, 33, 33, 49, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 33, 33, 33, 33, 33, 33, 50, 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, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000435752319 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 Building ZINC000435752319 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000435752319 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 621) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@@H]1CCCN1C1CCCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752319.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000435752319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752319 none O=C(NC[C@@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 23, 37, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 22, 22, 37, 37, 37, 37, 37, 37, 50, 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, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 622) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@@H]1CCCN1C1CCCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752319.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000435752319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752319 none O=C(NC[C@@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 33, 33, 33, 33, 33, 49, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 33, 33, 33, 33, 33, 33, 50, 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, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 623) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/623: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN1C1CCCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752319.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000435752319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752319 none O=C(NC[C@@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 23, 37, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 22, 22, 37, 37, 37, 37, 37, 37, 50, 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, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 624) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/624: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN1C1CCCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752319.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000435752319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752319 none O=C(NC[C@@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 33, 33, 33, 33, 33, 49, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 33, 33, 33, 33, 33, 33, 50, 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, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000435752319 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 Building ZINC000435752319 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000435752319 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 621) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@@H]1CCCN1C1CCCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752319.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000435752319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752319 none O=C(NC[C@@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 23, 37, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 22, 22, 37, 37, 37, 37, 37, 37, 50, 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, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 622) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@@H]1CCCN1C1CCCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752319.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000435752319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752319 none O=C(NC[C@@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 33, 33, 33, 33, 33, 49, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 33, 33, 33, 33, 33, 33, 50, 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, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 623) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/623: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN1C1CCCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752319.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000435752319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752319 none O=C(NC[C@@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 23, 37, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 22, 22, 37, 37, 37, 37, 37, 37, 50, 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, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 624) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/624: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN1C1CCCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752319.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000435752319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752319 none O=C(NC[C@@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 33, 33, 33, 33, 33, 49, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 33, 33, 33, 33, 33, 33, 50, 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, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000435752319 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 Building ZINC000435752319 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000435752319 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 621) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@@H]1CCCN1C1CCCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752319.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000435752319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752319 none O=C(NC[C@@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 23, 37, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 22, 22, 37, 37, 37, 37, 37, 37, 50, 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, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 622) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@@H]1CCCN1C1CCCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752319.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000435752319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752319 none O=C(NC[C@@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 33, 33, 33, 33, 33, 49, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 33, 33, 33, 33, 33, 33, 50, 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, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 623) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/623: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN1C1CCCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752319.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000435752319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752319 none O=C(NC[C@@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 23, 37, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 22, 22, 37, 37, 37, 37, 37, 37, 50, 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, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 624) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/624: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN1C1CCCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752319.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000435752319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752319 none O=C(NC[C@@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 33, 33, 33, 33, 33, 49, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 33, 33, 33, 33, 33, 33, 50, 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, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000435752319 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752319 Building ZINC000435752321 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000435752321 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/625 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCCN1C1CCCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000435752321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752321 none O=C(NC[C@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 32, 32, 32, 32, 32, 49, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 32, 32, 32, 32, 32, 32, 50, 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, 46, 47, 48]) total number of confs: 153 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/626 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/626' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCCN1C1CCCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000435752321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752321 none O=C(NC[C@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 23, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 22, 22, 38, 38, 38, 38, 38, 38, 50, 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, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/627 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/627' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCCN1C1CCCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752321.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000435752321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752321 none O=C(NC[C@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 32, 32, 32, 32, 32, 49, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 32, 32, 32, 32, 32, 32, 50, 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, 46, 47, 48]) total number of confs: 153 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/628 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/628' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCCN1C1CCCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752321.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000435752321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752321 none O=C(NC[C@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 23, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 22, 22, 38, 38, 38, 38, 38, 38, 50, 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, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000435752321 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 Building ZINC000435752321 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000435752321 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 625) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@H]1CCCN1C1CCCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000435752321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752321 none O=C(NC[C@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 32, 32, 32, 32, 32, 49, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 32, 32, 32, 32, 32, 32, 50, 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, 46, 47, 48]) total number of confs: 153 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 626) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@H]1CCCN1C1CCCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000435752321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752321 none O=C(NC[C@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 23, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 22, 22, 38, 38, 38, 38, 38, 38, 50, 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, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 627) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/627: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN1C1CCCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752321.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000435752321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752321 none O=C(NC[C@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 32, 32, 32, 32, 32, 49, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 32, 32, 32, 32, 32, 32, 50, 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, 46, 47, 48]) total number of confs: 153 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 628) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/628: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN1C1CCCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752321.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000435752321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752321 none O=C(NC[C@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 23, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 22, 22, 38, 38, 38, 38, 38, 38, 50, 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, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000435752321 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 Building ZINC000435752321 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000435752321 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 625) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@H]1CCCN1C1CCCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000435752321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752321 none O=C(NC[C@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 32, 32, 32, 32, 32, 49, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 32, 32, 32, 32, 32, 32, 50, 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, 46, 47, 48]) total number of confs: 153 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 626) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@H]1CCCN1C1CCCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000435752321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752321 none O=C(NC[C@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 23, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 22, 22, 38, 38, 38, 38, 38, 38, 50, 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, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 627) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/627: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN1C1CCCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752321.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000435752321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752321 none O=C(NC[C@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 32, 32, 32, 32, 32, 49, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 32, 32, 32, 32, 32, 32, 50, 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, 46, 47, 48]) total number of confs: 153 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 628) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/628: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN1C1CCCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752321.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000435752321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752321 none O=C(NC[C@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 23, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 22, 22, 38, 38, 38, 38, 38, 38, 50, 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, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000435752321 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 Building ZINC000435752321 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000435752321 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 625) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@H]1CCCN1C1CCCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000435752321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752321 none O=C(NC[C@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 32, 32, 32, 32, 32, 49, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 32, 32, 32, 32, 32, 32, 50, 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, 46, 47, 48]) total number of confs: 153 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 626) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@H]1CCCN1C1CCCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000435752321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752321 none O=C(NC[C@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 23, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 22, 22, 38, 38, 38, 38, 38, 38, 50, 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, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 627) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/627: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN1C1CCCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752321.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000435752321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752321 none O=C(NC[C@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 32, 32, 32, 32, 32, 49, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 32, 32, 32, 32, 32, 32, 50, 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, 46, 47, 48]) total number of confs: 153 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 628) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/628: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN1C1CCCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000435752321.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000435752321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000435752321 none O=C(NC[C@H]1CCCN1C1CCCCC1)[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.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 23, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 22, 22, 38, 38, 38, 38, 38, 38, 50, 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, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000435752321 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000435752321 Building ZINC000436323377 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323377' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323377 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436323377 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323377/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323377 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/629 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]1(C(=O)OCC)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000436323377.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436323377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000436323377 none CCC[C@]1(C(=O)OCC)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 10, 10, 10, 35, 35, 38, 42, 10, 10, 10, 6, 1, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 19, 19, 19, 19, 19, 19, 19, 42, 42, 42, 42, 42, 10, 10, 10, 10, 10, 10, 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, 44, 45]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323377 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323377/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323377 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/630 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/630' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]1(C(=O)OCC)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000436323377.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436323377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000436323377 none CCC[C@]1(C(=O)OCC)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 8, 8, 8, 30, 30, 35, 44, 8, 8, 8, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 18, 18, 18, 18, 18, 18, 18, 44, 44, 44, 44, 44, 8, 8, 8, 8, 8, 8, 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, 44, 45]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323377 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436323377 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323377/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323377/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323377 Building ZINC000436323377 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323377' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323377 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436323377 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323377/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323377 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 629) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCC[C@]1(C(=O)OCC)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000436323377.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436323377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000436323377 none CCC[C@]1(C(=O)OCC)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 10, 10, 10, 35, 35, 38, 42, 10, 10, 10, 6, 1, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 19, 19, 19, 19, 19, 19, 19, 42, 42, 42, 42, 42, 10, 10, 10, 10, 10, 10, 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, 44, 45]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323377 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323377/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323377 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 630) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCC[C@]1(C(=O)OCC)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000436323377.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436323377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000436323377 none CCC[C@]1(C(=O)OCC)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 8, 8, 8, 30, 30, 35, 44, 8, 8, 8, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 18, 18, 18, 18, 18, 18, 18, 44, 44, 44, 44, 44, 8, 8, 8, 8, 8, 8, 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, 44, 45]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323377 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436323377 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323377/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323377/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323377 Building ZINC000436323378 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323378' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323378 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436323378 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323378/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323378 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/631 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]1(C(=O)OCC)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000436323378.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436323378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000436323378 none CCC[C@@]1(C(=O)OCC)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 7, 7, 7, 27, 27, 32, 35, 7, 7, 7, 2, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 16, 16, 16, 16, 16, 16, 16, 35, 35, 35, 35, 35, 7, 7, 7, 7, 7, 7, 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, 44, 45]) total number of confs: 139 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323378 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323378/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323378 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/632 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/632' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]1(C(=O)OCC)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000436323378.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436323378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323378/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000436323378 none CCC[C@@]1(C(=O)OCC)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 10, 10, 10, 34, 34, 42, 44, 10, 10, 10, 3, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 18, 18, 18, 18, 18, 18, 18, 44, 44, 44, 44, 44, 10, 10, 10, 10, 10, 10, 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, 44, 45]) total number of confs: 154 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323378 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436323378 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323378/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323378/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323378 Building ZINC000436323378 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323378' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323378 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436323378 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323378/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323378 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 631) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCC[C@@]1(C(=O)OCC)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000436323378.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436323378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000436323378 none CCC[C@@]1(C(=O)OCC)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 7, 7, 7, 27, 27, 32, 35, 7, 7, 7, 2, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 16, 16, 16, 16, 16, 16, 16, 35, 35, 35, 35, 35, 7, 7, 7, 7, 7, 7, 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, 44, 45]) total number of confs: 139 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323378 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323378/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323378 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 632) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCC[C@@]1(C(=O)OCC)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000436323378.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436323378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323378/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000436323378 none CCC[C@@]1(C(=O)OCC)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 10, 10, 10, 34, 34, 42, 44, 10, 10, 10, 3, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 18, 18, 18, 18, 18, 18, 18, 44, 44, 44, 44, 44, 10, 10, 10, 10, 10, 10, 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, 44, 45]) total number of confs: 154 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323378 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436323378 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323378/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323378/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436323378 Building ZINC000436564149 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436564149' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436564149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436564149 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436564149/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436564149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/633 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/633' -> `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])c1ccc(O)cc1) `ZINC000436564149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436564149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436564149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000436564149 none O=C(Nc1ccc(OC(F)(F)F)cc1O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 12, 1, 1, 6, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 12, 12, 9, 12, 46, 50, 50, 50, 12, 12, 12, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 12, 12, 12, 24, 3, 3, 6, 3, 3] 200 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436564149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436564149/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436564149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/634 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/634' -> `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])c1ccc(O)cc1) `ZINC000436564149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436564149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436564149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000436564149 none O=C(Nc1ccc(OC(F)(F)F)cc1O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 12, 1, 1, 6, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 12, 12, 4, 12, 47, 50, 50, 50, 12, 12, 12, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 12, 12, 12, 24, 3, 3, 6, 3, 3] 200 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436564149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436564149 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436564149/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436564149/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436564149 Building ZINC000436564149 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436564149' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436564149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436564149 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436564149/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436564149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 633) grep: /scratch/xiaobo/83235/xao-8058115.15/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(Nc1ccc(OC(F)(F)F)cc1O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436564149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436564149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436564149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000436564149 none O=C(Nc1ccc(OC(F)(F)F)cc1O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 12, 1, 1, 6, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 12, 12, 9, 12, 46, 50, 50, 50, 12, 12, 12, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 12, 12, 12, 24, 3, 3, 6, 3, 3] 200 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436564149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436564149/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436564149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 634) grep: /scratch/xiaobo/83235/xao-8058115.15/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(Nc1ccc(OC(F)(F)F)cc1O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436564149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436564149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436564149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000436564149 none O=C(Nc1ccc(OC(F)(F)F)cc1O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 12, 1, 1, 6, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 12, 12, 4, 12, 47, 50, 50, 50, 12, 12, 12, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 12, 12, 12, 24, 3, 3, 6, 3, 3] 200 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436564149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436564149 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436564149/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436564149/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436564149 Building ZINC000436565500 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436565500' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436565500 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436565500 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436565500/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436565500 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/635 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc2c(CCNC(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)cn(C)c2c1) `ZINC000436565500.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436565500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436565500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000436565500 none Cc1ccc2c(CCNC(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)cn(C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 27, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 15, 15, 3, 3, 3, 6, 3, 3, 50, 50, 50, 50, 50] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/83235/xao-8058115.15/working/building/ZINC000436565500 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436565500/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436565500 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/636 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/636' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc2c(CCNC(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)cn(C)c2c1) `ZINC000436565500.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436565500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436565500/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000436565500 none Cc1ccc2c(CCNC(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)cn(C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 28, 16, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 16, 16, 3, 3, 3, 6, 3, 3, 50, 50, 50, 50, 50] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436565500 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436565500 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436565500/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436565500/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436565500 Building ZINC000436565500 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436565500' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436565500 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436565500 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436565500/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436565500 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 635) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc2c(CCNC(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)cn(C)c2c1) `ZINC000436565500.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436565500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436565500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000436565500 none Cc1ccc2c(CCNC(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)cn(C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 27, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 15, 15, 3, 3, 3, 6, 3, 3, 50, 50, 50, 50, 50] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/83235/xao-8058115.15/working/building/ZINC000436565500 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436565500/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436565500 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 636) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc2c(CCNC(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)cn(C)c2c1) `ZINC000436565500.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436565500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436565500/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000436565500 none Cc1ccc2c(CCNC(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)cn(C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 28, 16, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 16, 16, 3, 3, 3, 6, 3, 3, 50, 50, 50, 50, 50] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436565500 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436565500 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436565500/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436565500/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436565500 Building ZINC000535053981 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000535053981' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000535053981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535053981 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000535053981/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000535053981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/637 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)O1) `ZINC000535053981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535053981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000535053981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000535053981 none C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 12, 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, 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] 0 hydrogens 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, 13, 33, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 8, 6, 6, 6, 6, 33, 33, 33, 33, 33] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000535053981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000535053981/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000535053981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/638 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/638' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)O1) `ZINC000535053981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535053981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000535053981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000535053981 none C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 12, 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, 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] 0 hydrogens 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, 13, 33, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 7, 6, 6, 6, 6, 33, 33, 33, 33, 33] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000535053981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000535053981 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000535053981/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000535053981/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000535053981 Building ZINC000535053981 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000535053981' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000535053981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535053981 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000535053981/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000535053981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 637) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)O1) `ZINC000535053981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535053981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000535053981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000535053981 none C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 12, 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, 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] 0 hydrogens 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, 13, 33, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 8, 6, 6, 6, 6, 33, 33, 33, 33, 33] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000535053981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000535053981/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000535053981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 638) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)O1) `ZINC000535053981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535053981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000535053981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000535053981 none C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 12, 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, 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] 0 hydrogens 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, 13, 33, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 7, 6, 6, 6, 6, 33, 33, 33, 33, 33] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000535053981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000535053981 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000535053981/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000535053981/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000535053981 Building ZINC000436596119 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436596119' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436596119 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436596119 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436596119/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436596119 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/639 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[C@@H](c2ccccc2)O1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436596119.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436596119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436596119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436596119 none O=C(NC[C@H]1CC[C@@H](c2ccccc2)O1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 27, 47, 47, 47, 47, 47, 47, 50, 50, 47, 50, 50, 47, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 15, 15, 47, 47, 47, 47, 50, 50, 47, 50, 50, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436596119 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436596119/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436596119 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/640 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/640' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[C@@H](c2ccccc2)O1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436596119.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436596119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436596119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436596119 none O=C(NC[C@H]1CC[C@@H](c2ccccc2)O1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 25, 49, 49, 49, 49, 49, 49, 50, 50, 49, 50, 50, 49, 1, 1, 1, 3, 3, 1, 1, 3, 3, 2, 14, 14, 49, 49, 49, 49, 50, 50, 49, 50, 50, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 158 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436596119 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436596119 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436596119/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436596119/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436596119 Building ZINC000436596119 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436596119' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436596119 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436596119 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436596119/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436596119 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 639) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@H]1CC[C@@H](c2ccccc2)O1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436596119.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436596119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436596119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436596119 none O=C(NC[C@H]1CC[C@@H](c2ccccc2)O1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 27, 47, 47, 47, 47, 47, 47, 50, 50, 47, 50, 50, 47, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 15, 15, 47, 47, 47, 47, 50, 50, 47, 50, 50, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436596119 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436596119/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436596119 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 640) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@H]1CC[C@@H](c2ccccc2)O1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436596119.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436596119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436596119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436596119 none O=C(NC[C@H]1CC[C@@H](c2ccccc2)O1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 25, 49, 49, 49, 49, 49, 49, 50, 50, 49, 50, 50, 49, 1, 1, 1, 3, 3, 1, 1, 3, 3, 2, 14, 14, 49, 49, 49, 49, 50, 50, 49, 50, 50, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 158 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436596119 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436596119 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436596119/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436596119/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436596119 Building ZINC000436629052 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436629052' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436629052 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436629052 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436629052/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436629052 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/641 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc(F)c(Cl)cc1F)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436629052.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436629052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436629052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000436629052 none O=C(NCc1cc(F)c(Cl)cc1F)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 15, 1, 16, 1, 1, 15, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 15, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 15, 15, 50, 50, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436629052 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436629052/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436629052 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/642 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/642' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc(F)c(Cl)cc1F)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436629052.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436629052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436629052/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000436629052 none O=C(NCc1cc(F)c(Cl)cc1F)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 15, 1, 16, 1, 1, 15, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 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] 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, 17, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 17, 17, 50, 50, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436629052 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436629052 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436629052/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436629052/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436629052 Building ZINC000436629052 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436629052' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436629052 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436629052 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436629052/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436629052 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 641) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NCc1cc(F)c(Cl)cc1F)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436629052.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436629052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436629052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000436629052 none O=C(NCc1cc(F)c(Cl)cc1F)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 15, 1, 16, 1, 1, 15, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 15, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 15, 15, 50, 50, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436629052 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436629052/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436629052 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 642) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NCc1cc(F)c(Cl)cc1F)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436629052.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436629052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436629052/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000436629052 none O=C(NCc1cc(F)c(Cl)cc1F)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 15, 1, 16, 1, 1, 15, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 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] 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, 17, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 17, 17, 50, 50, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436629052 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436629052 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436629052/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436629052/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436629052 Building ZINC000436630885 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630885' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630885 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436630885 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630885/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630885 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/643 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)[C@H]1CCOc2c(NC(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)cccc21) `ZINC000436630885.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436630885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000436630885 none CN(C)[C@H]1CCOc2c(NC(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 7, 5, 5, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 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: [47, 45, 47, 45, 45, 45, 45, 45, 39, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 1, 6, 6, 45, 45, 45, 45, 47, 47, 47, 47, 47, 47, 45, 45, 45, 45, 11, 6, 6, 12, 6, 6, 45, 45, 45] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 103 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630885 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630885/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630885 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/644 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/644' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)[C@H]1CCOc2c(NC(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)cccc21) `ZINC000436630885.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436630885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630885/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000436630885 none CN(C)[C@H]1CCOc2c(NC(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 7, 5, 5, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [44, 43, 44, 43, 43, 43, 43, 43, 38, 9, 9, 1, 9, 1, 1, 1, 6, 6, 1, 1, 6, 6, 43, 43, 43, 43, 44, 44, 44, 44, 44, 44, 43, 43, 43, 43, 9, 6, 6, 12, 6, 6, 43, 43, 43] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 96 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630885 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436630885 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630885/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630885/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630885 Building ZINC000436630885 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630885' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630885 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436630885 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630885/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630885 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 643) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN(C)[C@H]1CCOc2c(NC(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)cccc21) `ZINC000436630885.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436630885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000436630885 none CN(C)[C@H]1CCOc2c(NC(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 7, 5, 5, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 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: [47, 45, 47, 45, 45, 45, 45, 45, 39, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 1, 6, 6, 45, 45, 45, 45, 47, 47, 47, 47, 47, 47, 45, 45, 45, 45, 11, 6, 6, 12, 6, 6, 45, 45, 45] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 103 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630885 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630885/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630885 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 644) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN(C)[C@H]1CCOc2c(NC(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)cccc21) `ZINC000436630885.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436630885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630885/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000436630885 none CN(C)[C@H]1CCOc2c(NC(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 7, 5, 5, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [44, 43, 44, 43, 43, 43, 43, 43, 38, 9, 9, 1, 9, 1, 1, 1, 6, 6, 1, 1, 6, 6, 43, 43, 43, 43, 44, 44, 44, 44, 44, 44, 43, 43, 43, 43, 9, 6, 6, 12, 6, 6, 43, 43, 43] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 96 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630885 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436630885 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630885/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630885/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630885 Building ZINC000436630886 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630886' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630886 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436630886 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630886/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630886 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/645 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)[C@@H]1CCOc2c(NC(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)cccc21) `ZINC000436630886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436630886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000436630886 none CN(C)[C@@H]1CCOc2c(NC(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 7, 5, 5, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 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: [43, 43, 43, 43, 43, 43, 43, 43, 40, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 1, 6, 6, 41, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 11, 6, 6, 12, 6, 6, 43, 43, 43] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 98 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630886 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630886/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630886 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/646 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/646' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)[C@@H]1CCOc2c(NC(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)cccc21) `ZINC000436630886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436630886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000436630886 none CN(C)[C@@H]1CCOc2c(NC(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 7, 5, 5, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [46, 45, 46, 45, 45, 45, 45, 45, 40, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 1, 6, 6, 42, 45, 45, 45, 46, 46, 46, 46, 46, 46, 45, 45, 45, 45, 11, 6, 6, 12, 6, 6, 45, 45, 45] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 108 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630886 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436630886 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630886/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630886/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630886 Building ZINC000436630886 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630886' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630886 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436630886 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630886/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630886 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 645) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN(C)[C@@H]1CCOc2c(NC(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)cccc21) `ZINC000436630886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436630886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000436630886 none CN(C)[C@@H]1CCOc2c(NC(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 7, 5, 5, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 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: [43, 43, 43, 43, 43, 43, 43, 43, 40, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 1, 6, 6, 41, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 11, 6, 6, 12, 6, 6, 43, 43, 43] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 98 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630886 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630886/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630886 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 646) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN(C)[C@@H]1CCOc2c(NC(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)cccc21) `ZINC000436630886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436630886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000436630886 none CN(C)[C@@H]1CCOc2c(NC(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 7, 5, 5, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [46, 45, 46, 45, 45, 45, 45, 45, 40, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 1, 6, 6, 42, 45, 45, 45, 46, 46, 46, 46, 46, 46, 45, 45, 45, 45, 11, 6, 6, 12, 6, 6, 45, 45, 45] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 108 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630886 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436630886 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630886/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630886/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436630886 Building ZINC000436635345 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635345' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635345 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436635345 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635345/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635345 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/647 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@@H]1c1ccccc1OC(F)F)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436635345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436635345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000436635345 none O=C(N[C@H]1C[C@@H]1c1ccccc1OC(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', 'H', 'C.ar', 'C.ar', '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', '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, 7, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 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, 3, 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: [2, 1, 2, 2, 10, 10, 10, 10, 10, 27, 27, 18, 27, 27, 27, 43, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 2, 10, 10, 27, 27, 27, 27, 50, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635345 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635345/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635345 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/648 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/648' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@@H]1c1ccccc1OC(F)F)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436635345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436635345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000436635345 none O=C(N[C@H]1C[C@@H]1c1ccccc1OC(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', 'H', 'C.ar', 'C.ar', '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', '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, 7, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 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, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 10, 10, 10, 10, 10, 27, 27, 17, 27, 27, 27, 46, 50, 50, 1, 1, 1, 2, 2, 1, 2, 2, 2, 3, 10, 10, 27, 27, 27, 27, 50, 2, 2, 4, 2, 2] 100 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635345 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436635345 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635345/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635345/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635345 Building ZINC000436635345 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635345' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635345 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436635345 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635345/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635345 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 647) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H]1C[C@@H]1c1ccccc1OC(F)F)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436635345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436635345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000436635345 none O=C(N[C@H]1C[C@@H]1c1ccccc1OC(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', 'H', 'C.ar', 'C.ar', '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', '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, 7, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 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, 3, 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: [2, 1, 2, 2, 10, 10, 10, 10, 10, 27, 27, 18, 27, 27, 27, 43, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 2, 10, 10, 27, 27, 27, 27, 50, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635345 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635345/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635345 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 648) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H]1C[C@@H]1c1ccccc1OC(F)F)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436635345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436635345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000436635345 none O=C(N[C@H]1C[C@@H]1c1ccccc1OC(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', 'H', 'C.ar', 'C.ar', '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', '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, 7, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 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, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 10, 10, 10, 10, 10, 27, 27, 17, 27, 27, 27, 46, 50, 50, 1, 1, 1, 2, 2, 1, 2, 2, 2, 3, 10, 10, 27, 27, 27, 27, 50, 2, 2, 4, 2, 2] 100 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635345 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436635345 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635345/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635345/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635345 Building ZINC000436635497 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635497' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635497 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436635497 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635497/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635497 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/649 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(c2ccsc2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436635497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436635497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436635497 none Cn1nc(c2ccsc2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 21, 50, 50, 50, 50, 21, 10, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 50, 50, 50, 21, 10, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635497 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635497/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635497 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/650 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/650' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(c2ccsc2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436635497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436635497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436635497 none Cn1nc(c2ccsc2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 20, 50, 50, 50, 50, 20, 9, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 20, 20, 50, 50, 50, 20, 9, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635497 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436635497 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635497/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635497/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635497 Building ZINC000436635497 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635497' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635497 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436635497 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635497/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635497 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 649) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cn1nc(c2ccsc2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436635497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436635497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436635497 none Cn1nc(c2ccsc2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 21, 50, 50, 50, 50, 21, 10, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 50, 50, 50, 21, 10, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635497 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635497/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635497 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 650) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cn1nc(c2ccsc2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436635497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436635497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436635497 none Cn1nc(c2ccsc2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 20, 50, 50, 50, 50, 20, 9, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 20, 20, 50, 50, 50, 20, 9, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635497 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436635497 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635497/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635497/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436635497 Building ZINC000436638703 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638703' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638703 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436638703 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638703/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638703 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/651 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(c2ccc(F)cc2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000436638703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436638703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436638703 none C[C@]1(c2ccc(F)cc2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 1, 1, 1, 1, 15, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 49, 49, 46, 47, 49, 49, 31, 31, 10, 1, 10, 1, 1, 1, 5, 5, 1, 1, 5, 5, 31, 31, 31, 31, 49, 49, 49, 49, 31, 31, 31, 31, 5, 5, 10, 5, 5, 31, 31] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 114 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638703 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638703/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638703 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/652 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/652' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(c2ccc(F)cc2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000436638703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436638703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436638703 none C[C@]1(c2ccc(F)cc2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 1, 1, 1, 1, 15, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [30, 30, 30, 49, 49, 47, 47, 49, 49, 30, 30, 9, 1, 9, 1, 1, 1, 4, 4, 1, 2, 4, 4, 30, 30, 30, 30, 49, 49, 49, 49, 30, 30, 30, 30, 4, 4, 8, 4, 4, 30, 30] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 107 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638703 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436638703 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638703/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638703/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638703 Building ZINC000436638703 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638703' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638703 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436638703 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638703/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638703 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 651) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/651: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(c2ccc(F)cc2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000436638703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436638703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436638703 none C[C@]1(c2ccc(F)cc2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 1, 1, 1, 1, 15, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 49, 49, 46, 47, 49, 49, 31, 31, 10, 1, 10, 1, 1, 1, 5, 5, 1, 1, 5, 5, 31, 31, 31, 31, 49, 49, 49, 49, 31, 31, 31, 31, 5, 5, 10, 5, 5, 31, 31] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 114 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638703 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638703/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638703 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 652) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/652: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(c2ccc(F)cc2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000436638703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436638703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436638703 none C[C@]1(c2ccc(F)cc2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 1, 1, 1, 1, 15, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [30, 30, 30, 49, 49, 47, 47, 49, 49, 30, 30, 9, 1, 9, 1, 1, 1, 4, 4, 1, 2, 4, 4, 30, 30, 30, 30, 49, 49, 49, 49, 30, 30, 30, 30, 4, 4, 8, 4, 4, 30, 30] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 107 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638703 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436638703 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638703/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638703/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638703 Building ZINC000436638704 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638704' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638704 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436638704 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638704/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638704 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/653 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(c2ccc(F)cc2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000436638704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436638704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436638704 none C[C@@]1(c2ccc(F)cc2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 1, 1, 1, 1, 15, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 50, 50, 32, 50, 50, 50, 32, 32, 9, 1, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 32, 32, 32, 32, 50, 50, 50, 50, 32, 32, 32, 32, 3, 3, 6, 3, 3, 32, 32] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 188 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638704 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638704/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638704 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/654 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/654' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(c2ccc(F)cc2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000436638704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436638704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436638704 none C[C@@]1(c2ccc(F)cc2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 1, 1, 1, 1, 15, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 49, 49, 33, 49, 49, 49, 32, 32, 10, 1, 10, 1, 1, 1, 3, 3, 1, 3, 3, 3, 32, 32, 32, 32, 49, 49, 49, 49, 32, 32, 32, 32, 3, 3, 6, 3, 3, 32, 32] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 181 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638704 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436638704 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638704/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638704/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638704 Building ZINC000436638704 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638704' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638704 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436638704 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638704/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638704 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 653) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/653: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(c2ccc(F)cc2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000436638704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436638704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436638704 none C[C@@]1(c2ccc(F)cc2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 1, 1, 1, 1, 15, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 50, 50, 32, 50, 50, 50, 32, 32, 9, 1, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 32, 32, 32, 32, 50, 50, 50, 50, 32, 32, 32, 32, 3, 3, 6, 3, 3, 32, 32] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 188 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638704 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638704/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638704 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 654) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/654: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(c2ccc(F)cc2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000436638704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436638704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436638704 none C[C@@]1(c2ccc(F)cc2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 1, 1, 1, 1, 15, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 49, 49, 33, 49, 49, 49, 32, 32, 10, 1, 10, 1, 1, 1, 3, 3, 1, 3, 3, 3, 32, 32, 32, 32, 49, 49, 49, 49, 32, 32, 32, 32, 3, 3, 6, 3, 3, 32, 32] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 181 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638704 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436638704 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638704/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638704/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638704 Building ZINC000436638939 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638939' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638939 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436638939 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638939/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638939 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/655 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1[C@]1(F)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000436638939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436638939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436638939 none Cc1ccccc1[C@]1(F)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', '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, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 30, 50, 50, 26, 26, 26, 26, 26, 4, 1, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 50, 50, 50, 50, 48, 50, 50, 26, 26, 26, 26, 3, 3, 6, 3, 3, 26, 26] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 175 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638939 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638939/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638939 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/656 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/656' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1[C@]1(F)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000436638939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436638939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436638939 none Cc1ccccc1[C@]1(F)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', '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, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 27, 50, 50, 27, 27, 27, 27, 27, 5, 1, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 2, 2, 4, 2, 2, 27, 27] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 187 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638939 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436638939 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638939/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638939/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638939 Building ZINC000436638939 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638939' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638939 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436638939 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638939/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638939 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 655) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccccc1[C@]1(F)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000436638939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436638939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436638939 none Cc1ccccc1[C@]1(F)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', '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, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 30, 50, 50, 26, 26, 26, 26, 26, 4, 1, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 50, 50, 50, 50, 48, 50, 50, 26, 26, 26, 26, 3, 3, 6, 3, 3, 26, 26] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 175 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638939 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638939/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638939 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 656) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccccc1[C@]1(F)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000436638939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436638939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436638939 none Cc1ccccc1[C@]1(F)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', '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, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 27, 50, 50, 27, 27, 27, 27, 27, 5, 1, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 2, 2, 4, 2, 2, 27, 27] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 187 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638939 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436638939 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638939/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638939/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638939 Building ZINC000436638940 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638940' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638940 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436638940 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638940/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638940 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/657 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1[C@@]1(F)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000436638940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436638940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436638940 none Cc1ccccc1[C@@]1(F)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', '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, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 27, 50, 50, 27, 27, 27, 27, 27, 5, 1, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 2, 2, 4, 2, 2, 27, 27] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 191 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638940 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638940/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638940 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/658 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/658' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1[C@@]1(F)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000436638940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436638940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436638940 none Cc1ccccc1[C@@]1(F)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', '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, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 27, 50, 50, 27, 27, 27, 27, 27, 4, 1, 8, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 2, 2, 4, 2, 2, 27, 27] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 178 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638940 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436638940 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638940/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638940/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638940 Building ZINC000436638940 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638940' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638940 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436638940 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638940/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638940 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 657) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccccc1[C@@]1(F)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000436638940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436638940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436638940 none Cc1ccccc1[C@@]1(F)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', '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, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 27, 50, 50, 27, 27, 27, 27, 27, 5, 1, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 2, 2, 4, 2, 2, 27, 27] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 191 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638940 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638940/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638940 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 658) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccccc1[C@@]1(F)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000436638940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436638940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436638940 none Cc1ccccc1[C@@]1(F)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', '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, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 27, 50, 50, 27, 27, 27, 27, 27, 4, 1, 8, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 2, 2, 4, 2, 2, 27, 27] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 178 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638940 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436638940 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638940/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638940/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436638940 Building ZINC000436641180 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641180' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641180 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436641180 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641180/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641180 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/659 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2c(cc1F)CC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436641180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436641180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436641180 none COc1cc2c(cc1F)CC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', '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, 15, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [46, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 12, 28, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 46, 46, 46, 28, 28, 28, 28, 28, 28, 6, 5, 5, 10, 5, 5] 100 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641180 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641180/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641180 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/660 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/660' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2c(cc1F)CC[C@@H]2NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436641180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436641180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436641180 none COc1cc2c(cc1F)CC[C@@H]2NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', '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, 15, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [42, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 14, 29, 7, 1, 7, 1, 1, 1, 5, 5, 1, 1, 5, 5, 42, 42, 42, 29, 29, 29, 29, 29, 29, 7, 5, 5, 10, 5, 5] 100 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: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641180 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436641180 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641180/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641180/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641180 Building ZINC000436641180 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641180' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641180 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436641180 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641180/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641180 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 659) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1cc2c(cc1F)CC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436641180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436641180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436641180 none COc1cc2c(cc1F)CC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', '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, 15, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [46, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 12, 28, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 46, 46, 46, 28, 28, 28, 28, 28, 28, 6, 5, 5, 10, 5, 5] 100 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641180 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641180/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641180 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 660) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1cc2c(cc1F)CC[C@@H]2NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436641180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436641180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436641180 none COc1cc2c(cc1F)CC[C@@H]2NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', '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, 15, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [42, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 14, 29, 7, 1, 7, 1, 1, 1, 5, 5, 1, 1, 5, 5, 42, 42, 42, 29, 29, 29, 29, 29, 29, 7, 5, 5, 10, 5, 5] 100 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: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641180 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436641180 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641180/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641180/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641180 Building ZINC000436641181 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641181' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641181 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436641181 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641181/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641181 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/661 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2c(cc1F)CC[C@H]2NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436641181.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436641181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436641181 none COc1cc2c(cc1F)CC[C@H]2NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', '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, 15, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [45, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 12, 27, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 45, 45, 45, 27, 27, 27, 27, 27, 27, 6, 6, 6, 12, 6, 6] 100 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: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641181 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641181/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641181 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/662 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/662' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2c(cc1F)CC[C@H]2NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436641181.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436641181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641181/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436641181 none COc1cc2c(cc1F)CC[C@H]2NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', '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, 15, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [47, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 12, 28, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 47, 47, 47, 28, 28, 28, 28, 28, 28, 6, 5, 5, 10, 5, 5] 100 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: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641181 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436641181 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641181/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641181/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641181 Building ZINC000436641181 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641181' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641181 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436641181 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641181/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641181 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 661) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1cc2c(cc1F)CC[C@H]2NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436641181.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436641181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436641181 none COc1cc2c(cc1F)CC[C@H]2NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', '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, 15, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [45, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 12, 27, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 45, 45, 45, 27, 27, 27, 27, 27, 27, 6, 6, 6, 12, 6, 6] 100 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: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641181 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641181/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641181 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 662) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1cc2c(cc1F)CC[C@H]2NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436641181.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436641181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641181/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436641181 none COc1cc2c(cc1F)CC[C@H]2NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', '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, 15, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [47, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 12, 28, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 47, 47, 47, 28, 28, 28, 28, 28, 28, 6, 5, 5, 10, 5, 5] 100 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: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641181 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436641181 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641181/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641181/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436641181 Building ZINC000436624148 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624148' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624148 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436624148 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624148/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624148 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/663 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/663' -> `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])c1ccc(O)cc1) `ZINC000436624148.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436624148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436624148 none O=C(N[C@H](c1cc(F)ccc1F)C(F)F)[C@]([O-])([SiH3])c1ccc(O)cc1 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', 'O.3', '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, 12, 1, 1, 6, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 10, 10, 37, 37, 37, 37, 37, 37, 37, 10, 35, 35, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 37, 37, 37, 35, 3, 3, 6, 3, 3] 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]) total number of confs: 180 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624148 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624148/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624148 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/664 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/664' -> `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])c1ccc(O)cc1) `ZINC000436624148.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436624148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624148/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436624148 none O=C(N[C@H](c1cc(F)ccc1F)C(F)F)[C@@]([O-])([SiH3])c1ccc(O)cc1 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', 'O.3', '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, 12, 1, 1, 6, 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] 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, 10, 10, 38, 38, 38, 38, 38, 38, 38, 10, 29, 29, 1, 1, 1, 3, 3, 1, 1, 3, 3, 5, 38, 38, 38, 29, 3, 3, 6, 3, 3] 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]) total number of confs: 171 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624148 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436624148 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624148/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624148/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624148 Building ZINC000436624148 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624148' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624148 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436624148 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624148/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624148 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 663) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H](c1cc(F)ccc1F)C(F)F)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436624148.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436624148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436624148 none O=C(N[C@H](c1cc(F)ccc1F)C(F)F)[C@]([O-])([SiH3])c1ccc(O)cc1 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', 'O.3', '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, 12, 1, 1, 6, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 10, 10, 37, 37, 37, 37, 37, 37, 37, 10, 35, 35, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 37, 37, 37, 35, 3, 3, 6, 3, 3] 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]) total number of confs: 180 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624148 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624148/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624148 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 664) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H](c1cc(F)ccc1F)C(F)F)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436624148.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436624148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624148/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436624148 none O=C(N[C@H](c1cc(F)ccc1F)C(F)F)[C@@]([O-])([SiH3])c1ccc(O)cc1 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', 'O.3', '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, 12, 1, 1, 6, 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] 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, 10, 10, 38, 38, 38, 38, 38, 38, 38, 10, 29, 29, 1, 1, 1, 3, 3, 1, 1, 3, 3, 5, 38, 38, 38, 29, 3, 3, 6, 3, 3] 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]) total number of confs: 171 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624148 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436624148 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624148/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624148/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624148 Building ZINC000436624149 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624149' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436624149 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624149/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/665 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/665' -> `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])c1ccc(O)cc1) `ZINC000436624149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436624149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436624149 none O=C(N[C@@H](c1cc(F)ccc1F)C(F)F)[C@]([O-])([SiH3])c1ccc(O)cc1 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', 'O.3', '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, 12, 1, 1, 6, 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] 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, 10, 10, 37, 37, 37, 37, 37, 37, 37, 10, 29, 29, 1, 1, 1, 3, 3, 1, 1, 3, 3, 5, 37, 37, 37, 29, 3, 3, 6, 3, 3] 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]) total number of confs: 170 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624149/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/666 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/666' -> `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])c1ccc(O)cc1) `ZINC000436624149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436624149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436624149 none O=C(N[C@@H](c1cc(F)ccc1F)C(F)F)[C@@]([O-])([SiH3])c1ccc(O)cc1 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', 'O.3', '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, 12, 1, 1, 6, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 10, 10, 39, 39, 39, 39, 39, 39, 39, 10, 34, 34, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 39, 39, 39, 34, 3, 3, 6, 3, 3] 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]) total number of confs: 183 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436624149 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624149/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624149/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624149 Building ZINC000436624149 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624149' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436624149 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624149/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 665) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@@H](c1cc(F)ccc1F)C(F)F)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436624149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436624149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436624149 none O=C(N[C@@H](c1cc(F)ccc1F)C(F)F)[C@]([O-])([SiH3])c1ccc(O)cc1 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', 'O.3', '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, 12, 1, 1, 6, 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] 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, 10, 10, 37, 37, 37, 37, 37, 37, 37, 10, 29, 29, 1, 1, 1, 3, 3, 1, 1, 3, 3, 5, 37, 37, 37, 29, 3, 3, 6, 3, 3] 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]) total number of confs: 170 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624149/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 666) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@@H](c1cc(F)ccc1F)C(F)F)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436624149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436624149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436624149 none O=C(N[C@@H](c1cc(F)ccc1F)C(F)F)[C@@]([O-])([SiH3])c1ccc(O)cc1 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', 'O.3', '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, 12, 1, 1, 6, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 10, 10, 39, 39, 39, 39, 39, 39, 39, 10, 34, 34, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 39, 39, 39, 34, 3, 3, 6, 3, 3] 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]) total number of confs: 183 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436624149 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624149/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624149/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436624149 Building ZINC000436689344 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689344' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689344 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436689344 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689344/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689344 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/667 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1ccccc1)c1ccncc1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436689344.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436689344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436689344 none O=C(N[C@H](c1ccccc1)c1ccncc1)[C@@]([O-])([SiH3])c1ccc(O)cc1 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.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 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, 3, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 12, 12, 29, 29, 29, 29, 29, 12, 41, 41, 12, 41, 41, 1, 1, 1, 5, 5, 1, 2, 5, 5, 6, 29, 29, 29, 29, 29, 41, 41, 41, 41, 5, 5, 10, 5, 5] 100 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 190 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689344 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689344/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689344 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/668 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/668' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1ccccc1)c1ccncc1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436689344.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436689344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436689344 none O=C(N[C@H](c1ccccc1)c1ccncc1)[C@]([O-])([SiH3])c1ccc(O)cc1 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.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 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, 3, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 12, 12, 30, 30, 12, 30, 30, 12, 39, 39, 20, 39, 39, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 30, 30, 14, 30, 30, 39, 39, 39, 39, 5, 5, 10, 5, 5] 100 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 218 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689344 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436689344 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689344/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689344/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689344 Building ZINC000436689344 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689344' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689344 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436689344 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689344/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689344 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 667) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H](c1ccccc1)c1ccncc1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436689344.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436689344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436689344 none O=C(N[C@H](c1ccccc1)c1ccncc1)[C@@]([O-])([SiH3])c1ccc(O)cc1 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.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 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, 3, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 12, 12, 29, 29, 29, 29, 29, 12, 41, 41, 12, 41, 41, 1, 1, 1, 5, 5, 1, 2, 5, 5, 6, 29, 29, 29, 29, 29, 41, 41, 41, 41, 5, 5, 10, 5, 5] 100 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 190 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689344 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689344/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689344 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 668) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H](c1ccccc1)c1ccncc1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436689344.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436689344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436689344 none O=C(N[C@H](c1ccccc1)c1ccncc1)[C@]([O-])([SiH3])c1ccc(O)cc1 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.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 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, 3, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 12, 12, 30, 30, 12, 30, 30, 12, 39, 39, 20, 39, 39, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 30, 30, 14, 30, 30, 39, 39, 39, 39, 5, 5, 10, 5, 5] 100 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 218 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689344 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436689344 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689344/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689344/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689344 Building ZINC000436689345 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689345' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689345 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436689345 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689345/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689345 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/669 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1ccccc1)c1ccncc1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436689345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436689345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436689345 none O=C(N[C@@H](c1ccccc1)c1ccncc1)[C@@]([O-])([SiH3])c1ccc(O)cc1 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.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 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, 3, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 12, 12, 31, 31, 12, 31, 31, 12, 40, 40, 12, 40, 40, 1, 1, 1, 5, 5, 5, 5, 5, 5, 6, 31, 31, 12, 31, 31, 40, 40, 40, 40, 5, 5, 10, 5, 5] 100 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 221 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689345 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689345/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689345 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/670 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/670' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1ccccc1)c1ccncc1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436689345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436689345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436689345 none O=C(N[C@@H](c1ccccc1)c1ccncc1)[C@]([O-])([SiH3])c1ccc(O)cc1 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.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 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, 3, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 12, 12, 30, 30, 12, 30, 30, 12, 42, 42, 42, 42, 42, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 30, 30, 12, 30, 30, 42, 42, 42, 42, 5, 5, 10, 5, 5] 100 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 180 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689345 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436689345 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689345/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689345/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689345 Building ZINC000436689345 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689345' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689345 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436689345 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689345/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689345 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 669) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@@H](c1ccccc1)c1ccncc1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436689345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436689345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436689345 none O=C(N[C@@H](c1ccccc1)c1ccncc1)[C@@]([O-])([SiH3])c1ccc(O)cc1 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.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 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, 3, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 12, 12, 31, 31, 12, 31, 31, 12, 40, 40, 12, 40, 40, 1, 1, 1, 5, 5, 5, 5, 5, 5, 6, 31, 31, 12, 31, 31, 40, 40, 40, 40, 5, 5, 10, 5, 5] 100 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 221 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689345 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689345/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689345 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 670) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@@H](c1ccccc1)c1ccncc1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436689345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436689345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436689345 none O=C(N[C@@H](c1ccccc1)c1ccncc1)[C@]([O-])([SiH3])c1ccc(O)cc1 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.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 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, 3, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 12, 12, 30, 30, 12, 30, 30, 12, 42, 42, 42, 42, 42, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 30, 30, 12, 30, 30, 42, 42, 42, 42, 5, 5, 10, 5, 5] 100 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 180 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689345 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436689345 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689345/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689345/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689345 Building ZINC000436689352 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689352' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689352 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436689352 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689352/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689352 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/671 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1c1ccc2c(c1)OCO2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436689352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436689352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436689352 none O=C(N1CCC[C@H]1c1ccc2c(c1)OCO2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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: [9, 1, 9, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 4, 4, 1, 1, 4, 4, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 4, 4, 8, 4, 4] 100 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 95 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689352 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689352/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689352 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/672 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/672' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1c1ccc2c(c1)OCO2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436689352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436689352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436689352 none O=C(N1CCC[C@H]1c1ccc2c(c1)OCO2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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: [9, 1, 9, 16, 16, 16, 16, 16, 16, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 5, 5, 1, 1, 5, 5, 16, 16, 16, 16, 16, 16, 48, 48, 48, 48, 48, 5, 5, 10, 5, 5] 100 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 99 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689352 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436689352 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689352/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689352/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689352 Building ZINC000436689352 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689352' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689352 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436689352 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689352/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689352 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 671) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCC[C@H]1c1ccc2c(c1)OCO2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436689352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436689352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436689352 none O=C(N1CCC[C@H]1c1ccc2c(c1)OCO2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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: [9, 1, 9, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 4, 4, 1, 1, 4, 4, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 4, 4, 8, 4, 4] 100 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 95 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689352 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689352/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689352 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 672) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCC[C@H]1c1ccc2c(c1)OCO2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436689352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436689352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436689352 none O=C(N1CCC[C@H]1c1ccc2c(c1)OCO2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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: [9, 1, 9, 16, 16, 16, 16, 16, 16, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 5, 5, 1, 1, 5, 5, 16, 16, 16, 16, 16, 16, 48, 48, 48, 48, 48, 5, 5, 10, 5, 5] 100 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 99 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689352 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436689352 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689352/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689352/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689352 Building ZINC000436689354 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689354' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689354 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436689354 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689354/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689354 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/673 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1c1ccc2c(c1)OCO2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436689354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436689354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436689354 none O=C(N1CCC[C@@H]1c1ccc2c(c1)OCO2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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: [9, 1, 9, 16, 16, 16, 16, 16, 16, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 4, 4, 1, 1, 4, 4, 16, 16, 16, 16, 16, 16, 46, 46, 46, 46, 46, 4, 4, 8, 4, 4] 100 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 91 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689354 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689354/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689354 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/674 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/674' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1c1ccc2c(c1)OCO2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436689354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436689354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436689354 none O=C(N1CCC[C@@H]1c1ccc2c(c1)OCO2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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: [9, 1, 9, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 3, 3, 3, 3, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 87 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689354 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436689354 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689354/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689354/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689354 Building ZINC000436689354 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689354' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689354 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436689354 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689354/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689354 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 673) grep: /scratch/xiaobo/83235/xao-8058115.15/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(N1CCC[C@@H]1c1ccc2c(c1)OCO2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436689354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436689354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436689354 none O=C(N1CCC[C@@H]1c1ccc2c(c1)OCO2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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: [9, 1, 9, 16, 16, 16, 16, 16, 16, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 4, 4, 1, 1, 4, 4, 16, 16, 16, 16, 16, 16, 46, 46, 46, 46, 46, 4, 4, 8, 4, 4] 100 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 91 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689354 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689354/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689354 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 674) grep: /scratch/xiaobo/83235/xao-8058115.15/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(N1CCC[C@@H]1c1ccc2c(c1)OCO2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436689354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436689354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436689354 none O=C(N1CCC[C@@H]1c1ccc2c(c1)OCO2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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: [9, 1, 9, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 3, 3, 3, 3, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 87 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689354 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436689354 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689354/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689354/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436689354 Building ZINC000436666246 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436666246' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436666246 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436666246 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436666246/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436666246 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/675 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2ccccn2)cs1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436666246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436666246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436666246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436666246 none O=C(Nc1nc(c2ccccn2)cs1)[C@@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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, 8, 1, 14, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 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, 3, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 21, 21, 21, 46, 46, 46, 46, 46, 21, 21, 1, 1, 1, 6, 6, 1, 1, 6, 6, 11, 46, 46, 46, 46, 21, 6, 6, 12, 6, 6] 96 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436666246 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436666246/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436666246 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/676 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/676' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2ccccn2)cs1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436666246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436666246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436666246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436666246 none O=C(Nc1nc(c2ccccn2)cs1)[C@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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, 8, 1, 14, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 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, 3, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large 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, 12, 6, 6] 94 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: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436666246 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436666246 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436666246/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436666246/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436666246 Building ZINC000436666246 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436666246' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436666246 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436666246 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436666246/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436666246 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 675) grep: /scratch/xiaobo/83235/xao-8058115.15/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(Nc1nc(c2ccccn2)cs1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436666246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436666246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436666246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436666246 none O=C(Nc1nc(c2ccccn2)cs1)[C@@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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, 8, 1, 14, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 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, 3, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 21, 21, 21, 46, 46, 46, 46, 46, 21, 21, 1, 1, 1, 6, 6, 1, 1, 6, 6, 11, 46, 46, 46, 46, 21, 6, 6, 12, 6, 6] 96 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436666246 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436666246/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436666246 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 676) grep: /scratch/xiaobo/83235/xao-8058115.15/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(Nc1nc(c2ccccn2)cs1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436666246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436666246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436666246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436666246 none O=C(Nc1nc(c2ccccn2)cs1)[C@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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, 8, 1, 14, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 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, 3, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large 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, 12, 6, 6] 94 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: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436666246 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436666246 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436666246/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436666246/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436666246 Building ZINC000436736024 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436736024' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436736024 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436736024 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436736024/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436736024 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/677 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)[C@H](Oc2ccccc2)C[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436736024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436736024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436736024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000436736024 none CC1(C)[C@H](Oc2ccccc2)C[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 13, 13, 13, 13, 13, 39, 50, 50, 39, 50, 50, 13, 4, 13, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 13, 13, 13, 13, 50, 50, 39, 50, 50, 13, 13, 3, 3, 3, 6, 3, 3] 100 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436736024 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436736024/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436736024 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/678 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/678' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)[C@H](Oc2ccccc2)C[C@@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436736024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436736024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436736024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000436736024 none CC1(C)[C@H](Oc2ccccc2)C[C@@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 15, 15, 45, 50, 50, 45, 50, 50, 15, 4, 15, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 50, 50, 45, 50, 50, 15, 15, 3, 3, 3, 6, 3, 3] 100 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 113 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436736024 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436736024 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436736024/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436736024/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436736024 Building ZINC000436736024 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436736024' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436736024 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436736024 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436736024/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436736024 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 677) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC1(C)[C@H](Oc2ccccc2)C[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436736024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436736024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436736024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000436736024 none CC1(C)[C@H](Oc2ccccc2)C[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 13, 13, 13, 13, 13, 39, 50, 50, 39, 50, 50, 13, 4, 13, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 13, 13, 13, 13, 50, 50, 39, 50, 50, 13, 13, 3, 3, 3, 6, 3, 3] 100 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436736024 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436736024/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436736024 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 678) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC1(C)[C@H](Oc2ccccc2)C[C@@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436736024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436736024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436736024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000436736024 none CC1(C)[C@H](Oc2ccccc2)C[C@@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 15, 15, 45, 50, 50, 45, 50, 50, 15, 4, 15, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 50, 50, 45, 50, 50, 15, 15, 3, 3, 3, 6, 3, 3] 100 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 113 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436736024 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436736024 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436736024/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436736024/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436736024 Building ZINC000436703249 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703249' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703249 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436703249 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703249/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703249 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/679 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)CCO2)ccc1F) `ZINC000436703249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436703249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000436703249 none Cc1cc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)CCO2)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 12, 1, 1, 1, 15, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 12, 12, 12, 12, 7, 2, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 50, 50, 12, 13, 50, 50, 50, 50, 12, 12, 3, 3, 6, 3, 3, 12, 12, 12, 12, 50, 50] 100 rigid atoms, others: [10, 11, 12] set([0, 1, 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, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703249 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703249/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703249 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/680 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/680' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)CCO2)ccc1F) `ZINC000436703249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436703249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000436703249 none Cc1cc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)CCO2)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 12, 1, 1, 1, 15, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 11, 11, 11, 11, 7, 2, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 11, 50, 50, 11, 13, 50, 50, 50, 50, 11, 11, 2, 2, 4, 2, 2, 11, 11, 11, 11, 50, 50] 100 rigid atoms, others: [10, 11, 12] set([0, 1, 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, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 145 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703249 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436703249 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703249/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703249/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703249 Building ZINC000436703249 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703249' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703249 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436703249 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703249/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703249 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 679) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1cc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)CCO2)ccc1F) `ZINC000436703249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436703249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000436703249 none Cc1cc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)CCO2)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 12, 1, 1, 1, 15, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 12, 12, 12, 12, 7, 2, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 50, 50, 12, 13, 50, 50, 50, 50, 12, 12, 3, 3, 6, 3, 3, 12, 12, 12, 12, 50, 50] 100 rigid atoms, others: [10, 11, 12] set([0, 1, 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, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703249 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703249/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703249 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 680) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1cc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)CCO2)ccc1F) `ZINC000436703249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436703249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000436703249 none Cc1cc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)CCO2)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 12, 1, 1, 1, 15, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 11, 11, 11, 11, 7, 2, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 11, 50, 50, 11, 13, 50, 50, 50, 50, 11, 11, 2, 2, 4, 2, 2, 11, 11, 11, 11, 50, 50] 100 rigid atoms, others: [10, 11, 12] set([0, 1, 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, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 145 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703249 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436703249 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703249/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703249/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703249 Building ZINC000436703253 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703253' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703253 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436703253 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703253/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703253 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/681 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc([C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)CCO2)ccc1F) `ZINC000436703253.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436703253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000436703253 none Cc1cc([C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)CCO2)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 12, 1, 1, 1, 15, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 11, 11, 11, 11, 7, 2, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 11, 50, 50, 13, 13, 50, 50, 50, 50, 11, 11, 2, 2, 4, 2, 2, 11, 11, 11, 11, 50, 50] 100 rigid atoms, others: [10, 11, 12] set([0, 1, 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, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 135 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703253 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703253/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703253 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/682 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/682' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc([C@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)CCO2)ccc1F) `ZINC000436703253.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436703253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703253/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000436703253 none Cc1cc([C@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)CCO2)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 12, 1, 1, 1, 15, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 12, 12, 12, 12, 7, 2, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 50, 50, 17, 15, 50, 50, 50, 50, 12, 12, 3, 3, 6, 3, 3, 12, 12, 12, 12, 50, 50] 100 rigid atoms, others: [10, 11, 12] set([0, 1, 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, 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/83235/xao-8058115.15/working/building/ZINC000436703253 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436703253 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703253/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703253/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703253 Building ZINC000436703253 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703253' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703253 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436703253 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703253/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703253 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 681) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1cc([C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)CCO2)ccc1F) `ZINC000436703253.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436703253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000436703253 none Cc1cc([C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)CCO2)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 12, 1, 1, 1, 15, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 11, 11, 11, 11, 7, 2, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 11, 50, 50, 13, 13, 50, 50, 50, 50, 11, 11, 2, 2, 4, 2, 2, 11, 11, 11, 11, 50, 50] 100 rigid atoms, others: [10, 11, 12] set([0, 1, 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, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 135 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703253 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703253/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703253 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 682) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1cc([C@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)CCO2)ccc1F) `ZINC000436703253.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436703253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703253/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000436703253 none Cc1cc([C@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)CCO2)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 12, 1, 1, 1, 15, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 12, 12, 12, 12, 7, 2, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 50, 50, 17, 15, 50, 50, 50, 50, 12, 12, 3, 3, 6, 3, 3, 12, 12, 12, 12, 50, 50] 100 rigid atoms, others: [10, 11, 12] set([0, 1, 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, 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/83235/xao-8058115.15/working/building/ZINC000436703253 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436703253 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703253/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703253/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436703253 Building ZINC000436787399 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436787399' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436787399 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436787399 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436787399/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436787399 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/683 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)c1cc(C(F)(F)F)on1) `ZINC000436787399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436787399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436787399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000436787399 none CC(C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)c1cc(C(F)(F)F)on1 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', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'N.2', '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, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 6, 3, 3, 6, 3, 3, 50] 100 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436787399 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436787399/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436787399 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/684 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/684' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)c1cc(C(F)(F)F)on1) `ZINC000436787399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436787399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436787399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000436787399 none CC(C)(NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)c1cc(C(F)(F)F)on1 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', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'N.2', '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, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 14, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 5, 3, 3, 6, 3, 3, 50] 100 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436787399 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436787399 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436787399/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436787399/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436787399 Building ZINC000436787399 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436787399' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436787399 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436787399 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436787399/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436787399 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 683) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)c1cc(C(F)(F)F)on1) `ZINC000436787399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436787399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436787399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000436787399 none CC(C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)c1cc(C(F)(F)F)on1 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', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'N.2', '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, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 6, 3, 3, 6, 3, 3, 50] 100 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436787399 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436787399/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436787399 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 684) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)c1cc(C(F)(F)F)on1) `ZINC000436787399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436787399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436787399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000436787399 none CC(C)(NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)c1cc(C(F)(F)F)on1 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', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'N.2', '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, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 14, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 5, 3, 3, 6, 3, 3, 50] 100 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436787399 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436787399 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436787399/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436787399/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436787399 Building ZINC000436808810 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436808810' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436808810 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436808810 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436808810/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436808810 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/685 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1O) `ZINC000436808810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436808810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436808810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000436808810 none CCOC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', '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.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, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 44, 44, 14, 44, 14, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 14, 50, 50, 50, 50, 50, 14, 3, 3, 3, 3, 3, 14, 14, 28] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436808810 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436808810/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436808810 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/686 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/686' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1O) `ZINC000436808810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436808810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436808810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000436808810 none CCOC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', '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.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, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 45, 15, 45, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 15, 15, 50, 50, 50, 50, 50, 15, 3, 3, 3, 3, 3, 15, 15, 30] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436808810 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436808810 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436808810/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436808810/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436808810 Building ZINC000436808810 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436808810' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436808810 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436808810 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436808810/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436808810 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 685) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCOC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1O) `ZINC000436808810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436808810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436808810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000436808810 none CCOC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', '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.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, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 44, 44, 14, 44, 14, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 14, 50, 50, 50, 50, 50, 14, 3, 3, 3, 3, 3, 14, 14, 28] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436808810 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436808810/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436808810 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 686) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCOC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1O) `ZINC000436808810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436808810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436808810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000436808810 none CCOC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', '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.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, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 45, 15, 45, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 15, 15, 50, 50, 50, 50, 50, 15, 3, 3, 3, 3, 3, 15, 15, 30] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436808810 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436808810 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436808810/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436808810/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436808810 Building ZINC000436770282 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436770282' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436770282 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436770282 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436770282/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436770282 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/687 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H](c2ccc(Cl)cc2)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436770282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436770282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436770282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436770282 none O=C(N1CCO[C@H](c2ccc(Cl)cc2)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [12, 2, 15, 30, 30, 30, 30, 30, 30, 49, 49, 30, 37, 49, 49, 30, 1, 1, 1, 5, 5, 1, 1, 5, 5, 30, 30, 30, 30, 49, 49, 49, 49, 30, 30, 5, 5, 10, 5, 5] 100 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436770282 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436770282/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436770282 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/688 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/688' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H](c2ccc(Cl)cc2)C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436770282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436770282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436770282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436770282 none O=C(N1CCO[C@H](c2ccc(Cl)cc2)C1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 14, 32, 32, 32, 32, 32, 32, 49, 49, 32, 38, 49, 49, 32, 1, 1, 1, 5, 5, 1, 1, 5, 5, 32, 32, 32, 32, 49, 49, 49, 49, 32, 32, 5, 5, 10, 5, 5] 100 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 166 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436770282 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436770282 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436770282/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436770282/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436770282 Building ZINC000436770282 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436770282' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436770282 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436770282 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436770282/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436770282 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 687) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCO[C@H](c2ccc(Cl)cc2)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436770282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436770282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436770282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436770282 none O=C(N1CCO[C@H](c2ccc(Cl)cc2)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [12, 2, 15, 30, 30, 30, 30, 30, 30, 49, 49, 30, 37, 49, 49, 30, 1, 1, 1, 5, 5, 1, 1, 5, 5, 30, 30, 30, 30, 49, 49, 49, 49, 30, 30, 5, 5, 10, 5, 5] 100 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436770282 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436770282/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436770282 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 688) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCO[C@H](c2ccc(Cl)cc2)C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436770282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436770282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436770282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436770282 none O=C(N1CCO[C@H](c2ccc(Cl)cc2)C1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 14, 32, 32, 32, 32, 32, 32, 49, 49, 32, 38, 49, 49, 32, 1, 1, 1, 5, 5, 1, 1, 5, 5, 32, 32, 32, 32, 49, 49, 49, 49, 32, 32, 5, 5, 10, 5, 5] 100 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 166 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436770282 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436770282 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436770282/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436770282/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436770282 Building ZINC000436777275 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436777275' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436777275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436777275 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436777275/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436777275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/689 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCN1CCCCCC1)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436777275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436777275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436777275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000436777275 none CC(C)N(CCN1CCCCCC1)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 9, 18, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 6, 3, 3] 100 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 103 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436777275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436777275/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436777275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/690 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/690' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCN1CCCCCC1)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436777275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436777275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436777275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000436777275 none CC(C)N(CCN1CCCCCC1)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 9, 18, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 6, 3, 3] 100 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 103 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436777275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436777275 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436777275/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436777275/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436777275 Building ZINC000436777275 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436777275' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436777275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436777275 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436777275/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436777275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 689) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/689: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCN1CCCCCC1)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436777275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436777275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436777275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000436777275 none CC(C)N(CCN1CCCCCC1)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 9, 18, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 6, 3, 3] 100 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 103 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436777275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436777275/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436777275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 690) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/690: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCN1CCCCCC1)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436777275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436777275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436777275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000436777275 none CC(C)N(CCN1CCCCCC1)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 9, 18, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 6, 3, 3] 100 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 103 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436777275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436777275 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436777275/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436777275/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436777275 Building ZINC000436840161 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436840161' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436840161 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436840161 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436840161/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436840161 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/691 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(c2cccnc2)s1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436840161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436840161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436840161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436840161 none O=C(Nc1ncc(c2cccnc2)s1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 14, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 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, 3, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 12, 12, 12, 12, 49, 49, 49, 49, 49, 12, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 12, 49, 49, 49, 49, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436840161 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436840161/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436840161 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/692 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/692' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(c2cccnc2)s1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436840161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436840161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436840161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436840161 none O=C(Nc1ncc(c2cccnc2)s1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 14, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 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, 3, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 12, 12, 12, 12, 50, 50, 50, 50, 50, 12, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 12, 50, 50, 50, 50, 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436840161 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436840161 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436840161/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436840161/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436840161 Building ZINC000436840161 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436840161' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436840161 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436840161 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436840161/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436840161 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 691) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(Nc1ncc(c2cccnc2)s1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436840161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436840161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436840161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436840161 none O=C(Nc1ncc(c2cccnc2)s1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 14, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 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, 3, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 12, 12, 12, 12, 49, 49, 49, 49, 49, 12, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 12, 49, 49, 49, 49, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436840161 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436840161/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436840161 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 692) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(Nc1ncc(c2cccnc2)s1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436840161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436840161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436840161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436840161 none O=C(Nc1ncc(c2cccnc2)s1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 14, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 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, 3, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 12, 12, 12, 12, 50, 50, 50, 50, 50, 12, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 12, 50, 50, 50, 50, 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436840161 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436840161 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436840161/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436840161/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436840161 Building ZINC000436842186 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436842186' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436842186 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436842186 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436842186/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436842186 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/693 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC(=O)c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)ccc2O1) `ZINC000436842186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436842186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436842186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000436842186 none CC1(C)CC(=O)c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)ccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 22, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 2, 5, 5, 22, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 5, 10, 5, 5, 42, 42] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436842186 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436842186/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436842186 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/694 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/694' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC(=O)c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)ccc2O1) `ZINC000436842186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436842186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436842186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000436842186 none CC1(C)CC(=O)c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)ccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 21, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 21, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 5, 10, 5, 5, 42, 42] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436842186 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436842186 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436842186/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436842186/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436842186 Building ZINC000436842186 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436842186' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436842186 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436842186 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436842186/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436842186 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 693) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC1(C)CC(=O)c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)ccc2O1) `ZINC000436842186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436842186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436842186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000436842186 none CC1(C)CC(=O)c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)ccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 22, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 2, 5, 5, 22, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 5, 10, 5, 5, 42, 42] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436842186 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436842186/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436842186 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 694) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC1(C)CC(=O)c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)ccc2O1) `ZINC000436842186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436842186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436842186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000436842186 none CC1(C)CC(=O)c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)ccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 21, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 21, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 5, 10, 5, 5, 42, 42] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436842186 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436842186 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436842186/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436842186/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436842186 Building ZINC000436880785 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436880785' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436880785 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436880785 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436880785/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436880785 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/695 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cc1) `ZINC000436880785.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436880785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436880785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000436880785 none CC(C)C(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cc1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.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, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 31, 50, 31, 31, 16, 12, 16, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 16, 50, 50, 50, 50, 50, 50, 50, 31, 16, 16, 4, 3, 3, 6, 3, 3, 16, 16] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436880785 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436880785/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436880785 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/696 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/696' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cc1) `ZINC000436880785.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436880785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436880785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000436880785 none CC(C)C(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cc1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.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, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 31, 50, 31, 32, 12, 7, 15, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 50, 50, 50, 50, 50, 50, 50, 32, 15, 15, 4, 3, 3, 6, 3, 3, 15, 15] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436880785 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436880785 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436880785/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436880785/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436880785 Building ZINC000436880785 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436880785' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436880785 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436880785 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436880785/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436880785 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 695) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/695: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cc1) `ZINC000436880785.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436880785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436880785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000436880785 none CC(C)C(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cc1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.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, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 31, 50, 31, 31, 16, 12, 16, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 16, 50, 50, 50, 50, 50, 50, 50, 31, 16, 16, 4, 3, 3, 6, 3, 3, 16, 16] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436880785 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436880785/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436880785 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 696) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/696: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cc1) `ZINC000436880785.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436880785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436880785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000436880785 none CC(C)C(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cc1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.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, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 31, 50, 31, 32, 12, 7, 15, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 50, 50, 50, 50, 50, 50, 50, 32, 15, 15, 4, 3, 3, 6, 3, 3, 15, 15] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436880785 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436880785 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436880785/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436880785/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436880785 Building ZINC000436902214 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902214' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902214 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436902214 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902214/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902214 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/697 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1Cc1cccc(F)c1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436902214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436902214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436902214 none O=C(N1CCC[C@H]1Cc1cccc(F)c1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 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, 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: [9, 1, 9, 16, 16, 16, 16, 16, 16, 24, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 16, 16, 24, 24, 50, 50, 50, 50, 3, 3, 6, 3, 3] 100 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: 134 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902214 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902214/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902214 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/698 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/698' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1Cc1cccc(F)c1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436902214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436902214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436902214 none O=C(N1CCC[C@H]1Cc1cccc(F)c1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 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, 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: [8, 1, 8, 14, 14, 14, 14, 14, 14, 27, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 14, 14, 14, 27, 27, 50, 50, 50, 50, 3, 3, 6, 3, 3] 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, 41]) total number of confs: 151 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902214 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436902214 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902214/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902214/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902214 Building ZINC000436902214 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902214' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902214 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436902214 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902214/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902214 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 697) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCC[C@H]1Cc1cccc(F)c1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436902214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436902214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436902214 none O=C(N1CCC[C@H]1Cc1cccc(F)c1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 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, 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: [9, 1, 9, 16, 16, 16, 16, 16, 16, 24, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 16, 16, 24, 24, 50, 50, 50, 50, 3, 3, 6, 3, 3] 100 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: 134 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902214 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902214/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902214 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 698) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCC[C@H]1Cc1cccc(F)c1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436902214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436902214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436902214 none O=C(N1CCC[C@H]1Cc1cccc(F)c1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 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, 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: [8, 1, 8, 14, 14, 14, 14, 14, 14, 27, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 14, 14, 14, 27, 27, 50, 50, 50, 50, 3, 3, 6, 3, 3] 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, 41]) total number of confs: 151 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902214 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436902214 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902214/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902214/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902214 Building ZINC000436902215 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902215' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902215 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436902215 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902215/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902215 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/699 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1Cc1cccc(F)c1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436902215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436902215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436902215 none O=C(N1CCC[C@@H]1Cc1cccc(F)c1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 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, 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: [8, 1, 8, 14, 14, 14, 14, 14, 14, 26, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 14, 14, 14, 26, 26, 50, 50, 50, 50, 3, 3, 6, 3, 3] 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, 41]) total number of confs: 147 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902215 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902215/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902215 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/700 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/700' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1Cc1cccc(F)c1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436902215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436902215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436902215 none O=C(N1CCC[C@@H]1Cc1cccc(F)c1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 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, 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: [9, 1, 9, 16, 16, 16, 16, 16, 16, 24, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 16, 16, 16, 16, 16, 24, 24, 50, 50, 50, 50, 3, 3, 6, 3, 3] 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, 41]) total number of confs: 138 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902215 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436902215 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902215/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902215/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902215 Building ZINC000436902215 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902215' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902215 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436902215 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902215/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902215 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 699) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCC[C@@H]1Cc1cccc(F)c1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436902215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436902215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436902215 none O=C(N1CCC[C@@H]1Cc1cccc(F)c1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 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, 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: [8, 1, 8, 14, 14, 14, 14, 14, 14, 26, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 14, 14, 14, 26, 26, 50, 50, 50, 50, 3, 3, 6, 3, 3] 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, 41]) total number of confs: 147 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902215 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902215/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902215 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 700) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCC[C@@H]1Cc1cccc(F)c1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436902215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436902215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436902215 none O=C(N1CCC[C@@H]1Cc1cccc(F)c1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 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, 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: [9, 1, 9, 16, 16, 16, 16, 16, 16, 24, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 16, 16, 16, 16, 16, 24, 24, 50, 50, 50, 50, 3, 3, 6, 3, 3] 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, 41]) total number of confs: 138 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902215 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436902215 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902215/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902215/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436902215 Building ZINC000436908856 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436908856' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436908856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436908856 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436908856/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436908856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/701 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(c2cccnc2)c1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436908856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436908856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436908856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436908856 none O=C(NCc1cccc(c2cccnc2)c1)[C@@]([O-])([SiH3])c1ccc(O)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', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 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, 3, 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: [2, 1, 2, 2, 9, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 30, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 32, 32, 32, 50, 50, 50, 50, 32, 2, 2, 4, 2, 2] 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: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436908856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436908856/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436908856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/702 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/702' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(c2cccnc2)c1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436908856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436908856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436908856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436908856 none O=C(NCc1cccc(c2cccnc2)c1)[C@]([O-])([SiH3])c1ccc(O)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', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 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, 3, 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: [2, 1, 2, 2, 10, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 30, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 34, 34, 34, 50, 50, 50, 50, 34, 2, 2, 4, 2, 2] 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: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436908856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436908856 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436908856/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436908856/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436908856 Building ZINC000436908856 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436908856' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436908856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436908856 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436908856/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436908856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 701) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NCc1cccc(c2cccnc2)c1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436908856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436908856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436908856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436908856 none O=C(NCc1cccc(c2cccnc2)c1)[C@@]([O-])([SiH3])c1ccc(O)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', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 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, 3, 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: [2, 1, 2, 2, 9, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 30, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 32, 32, 32, 50, 50, 50, 50, 32, 2, 2, 4, 2, 2] 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: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436908856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436908856/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436908856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 702) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NCc1cccc(c2cccnc2)c1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436908856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436908856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436908856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436908856 none O=C(NCc1cccc(c2cccnc2)c1)[C@]([O-])([SiH3])c1ccc(O)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', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 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, 3, 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: [2, 1, 2, 2, 10, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 30, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 34, 34, 34, 50, 50, 50, 50, 34, 2, 2, 4, 2, 2] 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: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436908856 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436908856 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436908856/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436908856/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436908856 Building ZINC000436890434 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436890434' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436890434 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436890434 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436890434/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436890434 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/703 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nc2ccccc2n1C1CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436890434.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436890434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436890434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436890434 none O=C(NCc1nc2ccccc2n1C1CC1)[C@@]([O-])([SiH3])c1ccc(O)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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 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, 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, 15, 41, 41, 41, 41, 41, 41, 41, 41, 41, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 15, 15, 41, 41, 41, 41, 50, 50, 50, 50, 50, 3, 3, 6, 3, 3] 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, 41]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436890434 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436890434/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436890434 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/704 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/704' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nc2ccccc2n1C1CC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436890434.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436890434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436890434/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436890434 none O=C(NCc1nc2ccccc2n1C1CC1)[C@]([O-])([SiH3])c1ccc(O)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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 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, 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, 16, 41, 41, 41, 41, 41, 41, 41, 41, 41, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 16, 16, 41, 41, 41, 41, 50, 50, 50, 50, 50, 3, 3, 6, 3, 3] 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, 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/83235/xao-8058115.15/working/building/ZINC000436890434 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436890434 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436890434/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436890434/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436890434 Building ZINC000436890434 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436890434' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436890434 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436890434 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436890434/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436890434 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 703) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NCc1nc2ccccc2n1C1CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436890434.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436890434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436890434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436890434 none O=C(NCc1nc2ccccc2n1C1CC1)[C@@]([O-])([SiH3])c1ccc(O)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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 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, 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, 15, 41, 41, 41, 41, 41, 41, 41, 41, 41, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 15, 15, 41, 41, 41, 41, 50, 50, 50, 50, 50, 3, 3, 6, 3, 3] 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, 41]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436890434 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436890434/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436890434 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 704) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NCc1nc2ccccc2n1C1CC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436890434.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436890434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436890434/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436890434 none O=C(NCc1nc2ccccc2n1C1CC1)[C@]([O-])([SiH3])c1ccc(O)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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 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, 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, 16, 41, 41, 41, 41, 41, 41, 41, 41, 41, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 16, 16, 41, 41, 41, 41, 50, 50, 50, 50, 50, 3, 3, 6, 3, 3] 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, 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/83235/xao-8058115.15/working/building/ZINC000436890434 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436890434 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436890434/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436890434/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436890434 Building ZINC000436894218 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436894218' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436894218 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436894218 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436894218/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436894218 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/705 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1c[nH]c2ccc(F)cc12)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436894218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436894218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436894218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436894218 none O=C(NCCc1c[nH]c2ccc(F)cc12)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 17, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 17, 17, 31, 31, 50, 50, 50, 50, 3, 3, 6, 3, 3] 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]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436894218 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436894218/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436894218 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/706 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/706' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1c[nH]c2ccc(F)cc12)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436894218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436894218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436894218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436894218 none O=C(NCCc1c[nH]c2ccc(F)cc12)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 17, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 17, 17, 31, 31, 50, 50, 50, 50, 3, 3, 6, 3, 3] 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]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436894218 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436894218 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436894218/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436894218/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436894218 Building ZINC000436894218 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436894218' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436894218 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436894218 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436894218/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436894218 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 705) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NCCc1c[nH]c2ccc(F)cc12)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436894218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436894218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436894218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436894218 none O=C(NCCc1c[nH]c2ccc(F)cc12)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 17, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 17, 17, 31, 31, 50, 50, 50, 50, 3, 3, 6, 3, 3] 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]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436894218 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436894218/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436894218 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 706) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NCCc1c[nH]c2ccc(F)cc12)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436894218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436894218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436894218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436894218 none O=C(NCCc1c[nH]c2ccc(F)cc12)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 17, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 17, 17, 31, 31, 50, 50, 50, 50, 3, 3, 6, 3, 3] 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]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436894218 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436894218 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436894218/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436894218/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436894218 Building ZINC000436895647 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436895647' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436895647 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436895647 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436895647/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436895647 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/707 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1OC1CCC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436895647.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436895647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436895647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000436895647 none O=C(NCc1ccccc1OC1CCC1)[C@@]([O-])([SiH3])c1ccc(O)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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 12, 32, 32, 32, 32, 32, 32, 40, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 12, 12, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 2, 2, 4, 2, 2] 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, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436895647 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436895647/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436895647 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/708 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/708' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1OC1CCC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436895647.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436895647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436895647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000436895647 none O=C(NCc1ccccc1OC1CCC1)[C@]([O-])([SiH3])c1ccc(O)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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 14, 35, 35, 22, 35, 35, 35, 45, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 14, 14, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 2, 2, 4, 2, 2] 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, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436895647 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436895647 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436895647/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436895647/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436895647 Building ZINC000436895647 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436895647' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436895647 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436895647 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436895647/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436895647 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 707) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/707: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1OC1CCC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436895647.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436895647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436895647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000436895647 none O=C(NCc1ccccc1OC1CCC1)[C@@]([O-])([SiH3])c1ccc(O)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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 12, 32, 32, 32, 32, 32, 32, 40, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 12, 12, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 2, 2, 4, 2, 2] 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, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436895647 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436895647/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436895647 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 708) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/708: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1OC1CCC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436895647.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436895647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436895647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000436895647 none O=C(NCc1ccccc1OC1CCC1)[C@]([O-])([SiH3])c1ccc(O)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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 14, 35, 35, 22, 35, 35, 35, 45, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 14, 14, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 2, 2, 4, 2, 2] 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, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436895647 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436895647 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436895647/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436895647/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436895647 Building ZINC000436898572 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436898572' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436898572 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436898572 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436898572/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436898572 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/709 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(Oc2ccc(F)cc2)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436898572.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436898572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436898572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436898572 none O=C(N1CCC(Oc2ccc(F)cc2)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 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, 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, 10, 10, 10, 10, 41, 50, 50, 49, 50, 50, 50, 10, 10, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 10, 10, 50, 50, 50, 50, 10, 10, 10, 10, 3, 3, 6, 3, 3] 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, 41, 42]) total number of confs: 93 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436898572 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436898572/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436898572 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/710 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/710' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(Oc2ccc(F)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436898572.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436898572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436898572/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436898572 none O=C(N1CCC(Oc2ccc(F)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 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, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 9, 9, 9, 9, 41, 50, 50, 47, 50, 50, 50, 9, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 9, 9, 9, 9, 50, 50, 50, 50, 9, 9, 9, 9, 3, 3, 6, 3, 3] 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, 41, 42]) total number of confs: 97 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436898572 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436898572 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436898572/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436898572/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436898572 Building ZINC000436898572 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436898572' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436898572 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436898572 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436898572/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436898572 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 709) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCC(Oc2ccc(F)cc2)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436898572.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436898572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436898572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436898572 none O=C(N1CCC(Oc2ccc(F)cc2)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 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, 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, 10, 10, 10, 10, 41, 50, 50, 49, 50, 50, 50, 10, 10, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 10, 10, 50, 50, 50, 50, 10, 10, 10, 10, 3, 3, 6, 3, 3] 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, 41, 42]) total number of confs: 93 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436898572 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436898572/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436898572 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 710) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCC(Oc2ccc(F)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436898572.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436898572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436898572/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436898572 none O=C(N1CCC(Oc2ccc(F)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 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, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 9, 9, 9, 9, 41, 50, 50, 47, 50, 50, 50, 9, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 9, 9, 9, 9, 50, 50, 50, 50, 9, 9, 9, 9, 3, 3, 6, 3, 3] 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, 41, 42]) total number of confs: 97 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436898572 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436898572 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436898572/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436898572/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436898572 Building ZINC000436916106 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916106' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916106 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436916106 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916106/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916106 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/711 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H](C)c1nc(CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cs1) `ZINC000436916106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436916106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436916106 none CCO[C@H](C)c1nc(CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 1, 8, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 22, 50, 50, 22, 22, 11, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 4, 4, 4, 1, 1, 2, 1, 1, 22] 100 rigid atoms, others: [38, 39, 41, 42, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 43]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916106 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916106/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916106 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/712 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/712' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H](C)c1nc(CN(C)C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cs1) `ZINC000436916106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436916106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436916106 none CCO[C@H](C)c1nc(CN(C)C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 1, 8, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 25, 50, 50, 25, 25, 13, 5, 2, 5, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 5, 5, 5, 1, 1, 2, 1, 1, 25] 100 rigid atoms, others: [38, 39, 41, 42, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 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/83235/xao-8058115.15/working/building/ZINC000436916106 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436916106 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916106/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916106/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916106 Building ZINC000436916106 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916106' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916106 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436916106 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916106/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916106 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 711) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCO[C@H](C)c1nc(CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cs1) `ZINC000436916106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436916106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436916106 none CCO[C@H](C)c1nc(CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 1, 8, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 22, 50, 50, 22, 22, 11, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 4, 4, 4, 1, 1, 2, 1, 1, 22] 100 rigid atoms, others: [38, 39, 41, 42, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 43]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916106 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916106/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916106 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 712) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCO[C@H](C)c1nc(CN(C)C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cs1) `ZINC000436916106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436916106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436916106 none CCO[C@H](C)c1nc(CN(C)C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 1, 8, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 25, 50, 50, 25, 25, 13, 5, 2, 5, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 5, 5, 5, 1, 1, 2, 1, 1, 25] 100 rigid atoms, others: [38, 39, 41, 42, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 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/83235/xao-8058115.15/working/building/ZINC000436916106 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436916106 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916106/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916106/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916106 Building ZINC000436916107 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916107' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916107 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436916107 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916107/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916107 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/713 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H](C)c1nc(CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cs1) `ZINC000436916107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436916107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436916107 none CCO[C@@H](C)c1nc(CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 1, 8, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 23, 50, 50, 23, 23, 12, 5, 2, 5, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 5, 5, 5, 1, 1, 2, 1, 1, 23] 100 rigid atoms, others: [38, 39, 41, 42, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 43]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916107 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916107/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916107 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/714 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/714' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H](C)c1nc(CN(C)C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cs1) `ZINC000436916107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436916107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436916107 none CCO[C@@H](C)c1nc(CN(C)C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 1, 8, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 49, 21, 49, 49, 21, 21, 11, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 50, 50, 50, 50, 50, 49, 49, 49, 11, 11, 4, 4, 4, 1, 1, 2, 1, 1, 21] 100 rigid atoms, others: [38, 39, 41, 42, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 43]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916107 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436916107 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916107/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916107/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916107 Building ZINC000436916107 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916107' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916107 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436916107 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916107/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916107 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 713) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCO[C@@H](C)c1nc(CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cs1) `ZINC000436916107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436916107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436916107 none CCO[C@@H](C)c1nc(CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 1, 8, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 23, 50, 50, 23, 23, 12, 5, 2, 5, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 5, 5, 5, 1, 1, 2, 1, 1, 23] 100 rigid atoms, others: [38, 39, 41, 42, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 43]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916107 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916107/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916107 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 714) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCO[C@@H](C)c1nc(CN(C)C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cs1) `ZINC000436916107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436916107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436916107 none CCO[C@@H](C)c1nc(CN(C)C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 1, 8, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 49, 21, 49, 49, 21, 21, 11, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 50, 50, 50, 50, 50, 49, 49, 49, 11, 11, 4, 4, 4, 1, 1, 2, 1, 1, 21] 100 rigid atoms, others: [38, 39, 41, 42, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 43]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916107 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436916107 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916107/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916107/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436916107 Building ZINC000436926202 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436926202' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436926202 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436926202 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436926202/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436926202 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/715 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[C@H](c2ccccc2)O1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436926202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436926202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436926202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436926202 none O=C(NC[C@H]1CC[C@H](c2ccccc2)O1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 27, 48, 48, 48, 48, 48, 48, 50, 50, 48, 50, 50, 48, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 17, 17, 48, 48, 48, 48, 50, 50, 48, 50, 50, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436926202 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436926202/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436926202 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/716 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/716' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[C@H](c2ccccc2)O1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436926202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436926202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436926202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436926202 none O=C(NC[C@H]1CC[C@H](c2ccccc2)O1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 25, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50, 46, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 16, 16, 46, 46, 46, 46, 50, 50, 46, 50, 50, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436926202 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436926202 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436926202/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436926202/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436926202 Building ZINC000436926202 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436926202' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436926202 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436926202 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436926202/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436926202 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 715) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@H]1CC[C@H](c2ccccc2)O1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436926202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436926202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436926202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436926202 none O=C(NC[C@H]1CC[C@H](c2ccccc2)O1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 27, 48, 48, 48, 48, 48, 48, 50, 50, 48, 50, 50, 48, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 17, 17, 48, 48, 48, 48, 50, 50, 48, 50, 50, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436926202 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436926202/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436926202 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 716) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@H]1CC[C@H](c2ccccc2)O1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436926202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436926202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436926202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436926202 none O=C(NC[C@H]1CC[C@H](c2ccccc2)O1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 25, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50, 46, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 16, 16, 46, 46, 46, 46, 50, 50, 46, 50, 50, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436926202 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436926202 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436926202/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436926202/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436926202 Building ZINC000436928098 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436928098' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436928098 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436928098 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436928098/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436928098 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/717 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(c2cccnc2)cc1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436928098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436928098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436928098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436928098 none O=C(NCc1ccc(c2cccnc2)cc1)[C@@]([O-])([SiH3])c1ccc(O)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', '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, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 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, 3, 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: [3, 1, 3, 3, 14, 29, 29, 22, 22, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 14, 14, 29, 29, 50, 50, 50, 50, 29, 29, 2, 2, 4, 2, 2] 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: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436928098 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436928098/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436928098 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/718 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/718' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(c2cccnc2)cc1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436928098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436928098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436928098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436928098 none O=C(NCc1ccc(c2cccnc2)cc1)[C@]([O-])([SiH3])c1ccc(O)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', '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, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 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, 3, 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: [3, 1, 3, 3, 14, 26, 26, 14, 20, 50, 50, 50, 50, 50, 26, 26, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 14, 14, 26, 26, 50, 50, 50, 50, 26, 26, 3, 3, 6, 3, 3] 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: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436928098 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436928098 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436928098/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436928098/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436928098 Building ZINC000436928098 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436928098' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436928098 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436928098 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436928098/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436928098 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 717) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NCc1ccc(c2cccnc2)cc1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436928098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436928098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436928098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436928098 none O=C(NCc1ccc(c2cccnc2)cc1)[C@@]([O-])([SiH3])c1ccc(O)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', '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, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 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, 3, 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: [3, 1, 3, 3, 14, 29, 29, 22, 22, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 14, 14, 29, 29, 50, 50, 50, 50, 29, 29, 2, 2, 4, 2, 2] 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: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436928098 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436928098/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436928098 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 718) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NCc1ccc(c2cccnc2)cc1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436928098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436928098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436928098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436928098 none O=C(NCc1ccc(c2cccnc2)cc1)[C@]([O-])([SiH3])c1ccc(O)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', '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, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 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, 3, 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: [3, 1, 3, 3, 14, 26, 26, 14, 20, 50, 50, 50, 50, 50, 26, 26, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 14, 14, 26, 26, 50, 50, 50, 50, 26, 26, 3, 3, 6, 3, 3] 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: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436928098 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436928098 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436928098/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436928098/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436928098 Building ZINC000436911287 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911287' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911287 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436911287 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911287/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911287 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/719 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(C1)OCc1ccccc12)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436911287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436911287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436911287 none O=C(N1CCC[C@@]2(C1)OCc1ccccc12)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7] 1 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [17, 2, 28, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 5, 5, 1, 1, 5, 5, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 5, 5, 10, 5, 5] 74 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: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911287 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911287/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911287 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/720 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/720' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(C1)OCc1ccccc12)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436911287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436911287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436911287 none O=C(N1CCC[C@@]2(C1)OCc1ccccc12)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7] 1 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [17, 2, 30, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 5, 5, 1, 1, 5, 5, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 5, 10, 5, 5] 84 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: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911287 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436911287 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911287/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911287/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911287 Building ZINC000436911287 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911287' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911287 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436911287 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911287/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911287 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 719) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(C1)OCc1ccccc12)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436911287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436911287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436911287 none O=C(N1CCC[C@@]2(C1)OCc1ccccc12)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7] 1 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [17, 2, 28, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 5, 5, 1, 1, 5, 5, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 5, 5, 10, 5, 5] 74 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: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911287 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911287/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911287 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 720) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/720: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(C1)OCc1ccccc12)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436911287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436911287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436911287 none O=C(N1CCC[C@@]2(C1)OCc1ccccc12)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7] 1 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [17, 2, 30, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 5, 5, 1, 1, 5, 5, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 5, 10, 5, 5] 84 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: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911287 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436911287 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911287/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911287/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911287 Building ZINC000436911288 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911288' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911288 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436911288 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911288/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911288 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/721 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(C1)OCc1ccccc12)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436911288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436911288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436911288 none O=C(N1CCC[C@]2(C1)OCc1ccccc12)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7] 1 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [17, 2, 30, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 4, 4, 1, 1, 4, 4, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 8, 4, 4] 94 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: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911288 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911288/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911288 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/722 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/722' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(C1)OCc1ccccc12)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436911288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436911288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436911288 none O=C(N1CCC[C@]2(C1)OCc1ccccc12)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7] 1 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [17, 2, 32, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 3, 3, 1, 2, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 3, 3, 6, 3, 3] 96 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: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911288 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436911288 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911288/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911288/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911288 Building ZINC000436911288 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911288' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911288 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436911288 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911288/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911288 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 721) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCC[C@]2(C1)OCc1ccccc12)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436911288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436911288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436911288 none O=C(N1CCC[C@]2(C1)OCc1ccccc12)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7] 1 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [17, 2, 30, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 4, 4, 1, 1, 4, 4, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 8, 4, 4] 94 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: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911288 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911288/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911288 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 722) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCC[C@]2(C1)OCc1ccccc12)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436911288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436911288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436911288 none O=C(N1CCC[C@]2(C1)OCc1ccccc12)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7] 1 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [17, 2, 32, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 3, 3, 1, 2, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 3, 3, 6, 3, 3] 96 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: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911288 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436911288 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911288/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911288/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436911288 Building ZINC000436912125 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000436912125 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/723 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436912125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912125 none CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [30, 18, 18, 18, 18, 18, 18, 48, 48, 48, 48, 48, 18, 18, 13, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 30, 18, 18, 48, 48, 48, 48, 48, 18, 18, 18, 18, 3, 3, 6, 3, 3] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 165 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/724 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/724' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436912125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912125 none CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [30, 18, 18, 18, 18, 18, 18, 48, 48, 48, 48, 48, 18, 18, 13, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 30, 18, 18, 48, 48, 48, 48, 48, 18, 18, 18, 18, 3, 3, 6, 3, 3] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 165 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/725 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/725' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912125.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000436912125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912125 none CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [30, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 22, 22, 14, 1, 15, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 30, 22, 22, 48, 48, 48, 48, 48, 22, 22, 22, 22, 3, 3, 6, 3, 3] 100 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/726 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/726' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912125.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000436912125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912125 none CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [30, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 22, 22, 14, 1, 15, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 30, 22, 22, 48, 48, 48, 48, 48, 22, 22, 22, 22, 3, 3, 6, 3, 3] 100 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436912125 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 Building ZINC000436912125 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000436912125 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 723) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436912125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912125 none CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [30, 18, 18, 18, 18, 18, 18, 48, 48, 48, 48, 48, 18, 18, 13, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 30, 18, 18, 48, 48, 48, 48, 48, 18, 18, 18, 18, 3, 3, 6, 3, 3] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 165 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 724) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/724: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436912125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912125 none CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [30, 18, 18, 18, 18, 18, 18, 48, 48, 48, 48, 48, 18, 18, 13, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 30, 18, 18, 48, 48, 48, 48, 48, 18, 18, 18, 18, 3, 3, 6, 3, 3] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 165 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 725) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/725: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912125.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000436912125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912125 none CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [30, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 22, 22, 14, 1, 15, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 30, 22, 22, 48, 48, 48, 48, 48, 22, 22, 22, 22, 3, 3, 6, 3, 3] 100 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 726) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/726: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912125.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000436912125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912125 none CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [30, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 22, 22, 14, 1, 15, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 30, 22, 22, 48, 48, 48, 48, 48, 22, 22, 22, 22, 3, 3, 6, 3, 3] 100 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436912125 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 Building ZINC000436912125 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000436912125 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 723) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436912125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912125 none CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [30, 18, 18, 18, 18, 18, 18, 48, 48, 48, 48, 48, 18, 18, 13, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 30, 18, 18, 48, 48, 48, 48, 48, 18, 18, 18, 18, 3, 3, 6, 3, 3] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 165 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 724) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/724: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436912125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912125 none CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [30, 18, 18, 18, 18, 18, 18, 48, 48, 48, 48, 48, 18, 18, 13, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 30, 18, 18, 48, 48, 48, 48, 48, 18, 18, 18, 18, 3, 3, 6, 3, 3] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 165 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 725) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/725: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912125.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000436912125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912125 none CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [30, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 22, 22, 14, 1, 15, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 30, 22, 22, 48, 48, 48, 48, 48, 22, 22, 22, 22, 3, 3, 6, 3, 3] 100 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 726) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/726: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912125.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000436912125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912125 none CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [30, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 22, 22, 14, 1, 15, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 30, 22, 22, 48, 48, 48, 48, 48, 22, 22, 22, 22, 3, 3, 6, 3, 3] 100 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436912125 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 Building ZINC000436912125 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000436912125 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 723) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436912125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912125 none CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [30, 18, 18, 18, 18, 18, 18, 48, 48, 48, 48, 48, 18, 18, 13, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 30, 18, 18, 48, 48, 48, 48, 48, 18, 18, 18, 18, 3, 3, 6, 3, 3] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 165 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 724) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/724: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436912125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912125 none CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [30, 18, 18, 18, 18, 18, 18, 48, 48, 48, 48, 48, 18, 18, 13, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 30, 18, 18, 48, 48, 48, 48, 48, 18, 18, 18, 18, 3, 3, 6, 3, 3] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 165 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 725) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/725: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912125.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000436912125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912125 none CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [30, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 22, 22, 14, 1, 15, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 30, 22, 22, 48, 48, 48, 48, 48, 22, 22, 22, 22, 3, 3, 6, 3, 3] 100 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 726) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/726: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912125.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000436912125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912125 none CC[C@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [30, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 22, 22, 14, 1, 15, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 30, 22, 22, 48, 48, 48, 48, 48, 22, 22, 22, 22, 3, 3, 6, 3, 3] 100 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436912125 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912125 Building ZINC000436912127 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000436912127 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/727 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436912127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912127 none CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [28, 19, 19, 19, 19, 19, 19, 47, 47, 47, 47, 47, 19, 19, 9, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 28, 19, 19, 47, 47, 47, 47, 47, 19, 19, 19, 19, 3, 3, 6, 3, 3] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 152 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/728 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/728' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436912127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912127 none CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [28, 19, 19, 19, 19, 19, 19, 47, 47, 47, 47, 47, 19, 19, 9, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 28, 19, 19, 47, 47, 47, 47, 47, 19, 19, 19, 19, 3, 3, 6, 3, 3] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 152 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/729 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/729' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912127.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000436912127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912127 none CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [28, 18, 18, 18, 18, 18, 18, 46, 46, 25, 46, 46, 18, 18, 9, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 28, 18, 18, 46, 46, 25, 46, 46, 18, 18, 18, 18, 3, 3, 6, 3, 3] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 189 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/730 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/730' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912127.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000436912127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912127 none CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [28, 18, 18, 18, 18, 18, 18, 46, 46, 25, 46, 46, 18, 18, 9, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 28, 18, 18, 46, 46, 25, 46, 46, 18, 18, 18, 18, 3, 3, 6, 3, 3] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 189 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436912127 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 Building ZINC000436912127 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000436912127 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 727) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/727: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436912127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912127 none CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [28, 19, 19, 19, 19, 19, 19, 47, 47, 47, 47, 47, 19, 19, 9, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 28, 19, 19, 47, 47, 47, 47, 47, 19, 19, 19, 19, 3, 3, 6, 3, 3] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 152 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 728) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/728: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436912127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912127 none CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [28, 19, 19, 19, 19, 19, 19, 47, 47, 47, 47, 47, 19, 19, 9, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 28, 19, 19, 47, 47, 47, 47, 47, 19, 19, 19, 19, 3, 3, 6, 3, 3] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 152 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 729) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/729: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912127.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000436912127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912127 none CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [28, 18, 18, 18, 18, 18, 18, 46, 46, 25, 46, 46, 18, 18, 9, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 28, 18, 18, 46, 46, 25, 46, 46, 18, 18, 18, 18, 3, 3, 6, 3, 3] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 189 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 730) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/730: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912127.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000436912127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912127 none CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [28, 18, 18, 18, 18, 18, 18, 46, 46, 25, 46, 46, 18, 18, 9, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 28, 18, 18, 46, 46, 25, 46, 46, 18, 18, 18, 18, 3, 3, 6, 3, 3] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 189 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436912127 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 Building ZINC000436912127 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000436912127 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 727) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/727: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436912127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912127 none CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [28, 19, 19, 19, 19, 19, 19, 47, 47, 47, 47, 47, 19, 19, 9, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 28, 19, 19, 47, 47, 47, 47, 47, 19, 19, 19, 19, 3, 3, 6, 3, 3] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 152 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 728) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/728: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436912127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912127 none CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [28, 19, 19, 19, 19, 19, 19, 47, 47, 47, 47, 47, 19, 19, 9, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 28, 19, 19, 47, 47, 47, 47, 47, 19, 19, 19, 19, 3, 3, 6, 3, 3] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 152 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 729) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/729: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912127.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000436912127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912127 none CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [28, 18, 18, 18, 18, 18, 18, 46, 46, 25, 46, 46, 18, 18, 9, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 28, 18, 18, 46, 46, 25, 46, 46, 18, 18, 18, 18, 3, 3, 6, 3, 3] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 189 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 730) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/730: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912127.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000436912127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912127 none CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [28, 18, 18, 18, 18, 18, 18, 46, 46, 25, 46, 46, 18, 18, 9, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 28, 18, 18, 46, 46, 25, 46, 46, 18, 18, 18, 18, 3, 3, 6, 3, 3] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 189 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436912127 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 Building ZINC000436912127 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000436912127 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 727) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/727: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436912127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912127 none CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [28, 19, 19, 19, 19, 19, 19, 47, 47, 47, 47, 47, 19, 19, 9, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 28, 19, 19, 47, 47, 47, 47, 47, 19, 19, 19, 19, 3, 3, 6, 3, 3] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 152 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 728) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/728: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436912127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912127 none CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [28, 19, 19, 19, 19, 19, 19, 47, 47, 47, 47, 47, 19, 19, 9, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 28, 19, 19, 47, 47, 47, 47, 47, 19, 19, 19, 19, 3, 3, 6, 3, 3] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 152 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 729) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/729: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912127.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000436912127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912127 none CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [28, 18, 18, 18, 18, 18, 18, 46, 46, 25, 46, 46, 18, 18, 9, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 28, 18, 18, 46, 46, 25, 46, 46, 18, 18, 18, 18, 3, 3, 6, 3, 3] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 189 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 730) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/730: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436912127.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000436912127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000436912127 none CC[C@@H]1CN(c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 7, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 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: [28, 18, 18, 18, 18, 18, 18, 46, 46, 25, 46, 46, 18, 18, 9, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 28, 18, 18, 46, 46, 25, 46, 46, 18, 18, 18, 18, 3, 3, 6, 3, 3] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 189 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436912127 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436912127 Building ZINC000436950675 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436950675' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436950675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436950675 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436950675/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436950675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/731 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)c(Cl)c1) `ZINC000436950675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436950675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436950675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000436950675 none COc1ccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(O)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', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 43, 43, 43, 43, 34, 16, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 43, 43, 43, 50, 50, 50, 43, 43, 34, 34, 16, 16, 3, 3, 3, 6, 3, 3, 43] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436950675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436950675/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436950675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/732 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/732' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)c(Cl)c1) `ZINC000436950675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436950675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436950675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000436950675 none COc1ccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(O)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', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 34, 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, 6, 3, 3, 44] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436950675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436950675 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436950675/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436950675/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436950675 Building ZINC000436950675 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436950675' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436950675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436950675 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436950675/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436950675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 731) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)c(Cl)c1) `ZINC000436950675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436950675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436950675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000436950675 none COc1ccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(O)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', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 43, 43, 43, 43, 34, 16, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 43, 43, 43, 50, 50, 50, 43, 43, 34, 34, 16, 16, 3, 3, 3, 6, 3, 3, 43] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436950675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436950675/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436950675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 732) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)c(Cl)c1) `ZINC000436950675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436950675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436950675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000436950675 none COc1ccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(O)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', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 34, 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, 6, 3, 3, 44] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436950675 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436950675 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436950675/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436950675/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436950675 Building ZINC000436941571 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941571' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941571 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436941571 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941571/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941571 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/733 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(c2nc3ccccc3s2)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436941571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436941571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000436941571 none O=C(N1CC(c2nc3ccccc3s2)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 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] 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, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 14, 50, 50, 50, 50, 14, 14, 2, 2, 4, 2, 2] 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, 35, 36, 37]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941571 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941571/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941571 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/734 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/734' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(c2nc3ccccc3s2)C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436941571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436941571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000436941571 none O=C(N1CC(c2nc3ccccc3s2)C1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 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] 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, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 2, 2, 1, 1, 2, 2, 13, 13, 13, 50, 50, 50, 50, 13, 13, 2, 2, 4, 2, 2] 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, 35, 36, 37]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941571 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436941571 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941571/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941571/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941571 Building ZINC000436941571 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941571' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941571 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436941571 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941571/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941571 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 733) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CC(c2nc3ccccc3s2)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436941571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436941571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000436941571 none O=C(N1CC(c2nc3ccccc3s2)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 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] 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, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 14, 50, 50, 50, 50, 14, 14, 2, 2, 4, 2, 2] 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, 35, 36, 37]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941571 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941571/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941571 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 734) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CC(c2nc3ccccc3s2)C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436941571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436941571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000436941571 none O=C(N1CC(c2nc3ccccc3s2)C1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 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] 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, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 2, 2, 1, 1, 2, 2, 13, 13, 13, 50, 50, 50, 50, 13, 13, 2, 2, 4, 2, 2] 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, 35, 36, 37]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941571 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436941571 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941571/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941571/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941571 Building ZINC000436941688 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941688' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941688 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436941688 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941688/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941688 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/735 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(Cc2ccccc2Cl)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436941688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436941688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436941688 none O=C(N1CC(Cc2ccccc2Cl)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 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: [2, 1, 4, 14, 14, 14, 32, 50, 50, 46, 50, 50, 50, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 32, 32, 50, 50, 50, 50, 14, 14, 3, 3, 6, 3, 3] 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, 36, 37, 38]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941688 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941688/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941688 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/736 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/736' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(Cc2ccccc2Cl)C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436941688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436941688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436941688 none O=C(N1CC(Cc2ccccc2Cl)C1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 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: [2, 1, 4, 15, 15, 15, 35, 50, 50, 35, 50, 50, 50, 15, 1, 1, 1, 3, 3, 3, 3, 3, 3, 15, 15, 15, 35, 35, 50, 50, 50, 50, 15, 15, 3, 3, 6, 3, 3] 100 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941688 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436941688 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941688/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941688/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941688 Building ZINC000436941688 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941688' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941688 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436941688 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941688/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941688 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 735) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CC(Cc2ccccc2Cl)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436941688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436941688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436941688 none O=C(N1CC(Cc2ccccc2Cl)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 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: [2, 1, 4, 14, 14, 14, 32, 50, 50, 46, 50, 50, 50, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 32, 32, 50, 50, 50, 50, 14, 14, 3, 3, 6, 3, 3] 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, 36, 37, 38]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941688 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941688/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941688 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 736) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CC(Cc2ccccc2Cl)C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436941688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436941688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436941688 none O=C(N1CC(Cc2ccccc2Cl)C1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 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: [2, 1, 4, 15, 15, 15, 35, 50, 50, 35, 50, 50, 50, 15, 1, 1, 1, 3, 3, 3, 3, 3, 3, 15, 15, 15, 35, 35, 50, 50, 50, 50, 15, 15, 3, 3, 6, 3, 3] 100 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941688 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436941688 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941688/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941688/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436941688 Building ZINC000436942272 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942272' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942272 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436942272 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942272/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942272 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/737 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1c1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cc1) `ZINC000436942272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436942272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436942272 none Cc1nccn1c1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 8, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 22, 18, 28, 28, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 28, 28, 50, 50, 50, 50, 50, 28, 28, 8, 8, 8, 4, 3, 3, 6, 3, 3, 28, 28] 100 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: 146 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942272 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942272/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942272 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/738 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/738' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1c1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cc1) `ZINC000436942272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436942272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436942272 none Cc1nccn1c1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 8, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 26, 17, 30, 30, 9, 5, 9, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 50, 50, 50, 50, 50, 30, 30, 9, 9, 9, 5, 3, 3, 6, 3, 3, 30, 30] 100 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: 165 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942272 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436942272 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942272/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942272/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942272 Building ZINC000436942272 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942272' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942272 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436942272 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942272/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942272 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 737) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nccn1c1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cc1) `ZINC000436942272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436942272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436942272 none Cc1nccn1c1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 8, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 22, 18, 28, 28, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 28, 28, 50, 50, 50, 50, 50, 28, 28, 8, 8, 8, 4, 3, 3, 6, 3, 3, 28, 28] 100 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: 146 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942272 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942272/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942272 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 738) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nccn1c1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cc1) `ZINC000436942272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436942272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436942272 none Cc1nccn1c1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 8, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 26, 17, 30, 30, 9, 5, 9, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 50, 50, 50, 50, 50, 30, 30, 9, 9, 9, 5, 3, 3, 6, 3, 3, 30, 30] 100 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: 165 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942272 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436942272 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942272/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942272/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942272 Building ZINC000436942275 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942275' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436942275 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942275/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/739 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1c1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cc1) `ZINC000436942275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436942275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436942275 none Cc1nccn1c1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 8, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 21, 16, 29, 29, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 50, 50, 50, 50, 50, 29, 29, 8, 8, 8, 4, 3, 3, 6, 3, 3, 29, 29] 100 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: 161 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942275/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/740 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/740' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1c1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cc1) `ZINC000436942275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436942275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436942275 none Cc1nccn1c1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 8, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 22, 16, 28, 28, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 28, 28, 50, 50, 50, 50, 50, 28, 28, 8, 8, 8, 4, 3, 3, 6, 3, 3, 28, 28] 100 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: 156 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436942275 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942275/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942275/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942275 Building ZINC000436942275 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942275' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436942275 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942275/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 739) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nccn1c1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cc1) `ZINC000436942275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436942275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436942275 none Cc1nccn1c1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 8, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 21, 16, 29, 29, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 50, 50, 50, 50, 50, 29, 29, 8, 8, 8, 4, 3, 3, 6, 3, 3, 29, 29] 100 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: 161 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942275/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 740) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nccn1c1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cc1) `ZINC000436942275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436942275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436942275 none Cc1nccn1c1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 8, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 22, 16, 28, 28, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 28, 28, 50, 50, 50, 50, 50, 28, 28, 8, 8, 8, 4, 3, 3, 6, 3, 3, 28, 28] 100 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: 156 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436942275 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942275/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942275/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942275 Building ZINC000436942913 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942913' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942913 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436942913 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942913/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942913 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/741 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@@H]1Oc2ccccc2[C@H]1C) `ZINC000436942913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436942913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000436942913 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [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, 10, 5, 5, 49, 49, 49, 49, 49, 49, 49] 100 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 163 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942913 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942913/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942913 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/742 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/742' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@@H]1Oc2ccccc2[C@H]1C) `ZINC000436942913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436942913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000436942913 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [22, 5, 22, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 5, 4, 4, 8, 4, 4, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942913 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436942913 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942913/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942913/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942913 Building ZINC000436942913 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942913' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942913 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436942913 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942913/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942913 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 741) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/741: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@@H]1Oc2ccccc2[C@H]1C) `ZINC000436942913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436942913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000436942913 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [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, 10, 5, 5, 49, 49, 49, 49, 49, 49, 49] 100 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 163 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942913 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942913/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942913 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 742) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/742: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@@H]1Oc2ccccc2[C@H]1C) `ZINC000436942913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436942913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000436942913 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [22, 5, 22, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 5, 4, 4, 8, 4, 4, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942913 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436942913 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942913/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942913/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942913 Building ZINC000436942915 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942915' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942915 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436942915 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942915/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942915 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/743 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@@H]1Oc2ccccc2[C@@H]1C) `ZINC000436942915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436942915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000436942915 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [21, 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, 10, 5, 5, 49, 49, 49, 49, 49, 49, 49] 100 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 157 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942915 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942915/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942915 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/744 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/744' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@@H]1Oc2ccccc2[C@@H]1C) `ZINC000436942915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436942915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000436942915 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [24, 6, 24, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 6, 5, 5, 10, 5, 5, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 167 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942915 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436942915 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942915/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942915/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942915 Building ZINC000436942915 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942915' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942915 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436942915 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942915/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942915 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 743) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@@H]1Oc2ccccc2[C@@H]1C) `ZINC000436942915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436942915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000436942915 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [21, 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, 10, 5, 5, 49, 49, 49, 49, 49, 49, 49] 100 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 157 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942915 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942915/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942915 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 744) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@@H]1Oc2ccccc2[C@@H]1C) `ZINC000436942915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436942915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000436942915 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [24, 6, 24, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 6, 5, 5, 10, 5, 5, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 167 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942915 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436942915 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942915/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942915/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942915 Building ZINC000436942917 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942917' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942917 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436942917 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942917/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942917 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/745 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@H]1Oc2ccccc2[C@@H]1C) `ZINC000436942917.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436942917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000436942917 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 6, 16, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 6, 4, 4, 8, 4, 4, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 150 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942917 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942917/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942917 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/746 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/746' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@H]1Oc2ccccc2[C@@H]1C) `ZINC000436942917.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436942917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000436942917 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [18, 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, 10, 5, 5, 49, 49, 49, 49, 49, 49, 49] 100 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 166 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942917 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436942917 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942917/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942917/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942917 Building ZINC000436942917 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942917' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942917 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436942917 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942917/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942917 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 745) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@H]1Oc2ccccc2[C@@H]1C) `ZINC000436942917.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436942917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000436942917 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 6, 16, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 6, 4, 4, 8, 4, 4, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 150 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942917 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942917/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942917 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 746) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@H]1Oc2ccccc2[C@@H]1C) `ZINC000436942917.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436942917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000436942917 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [18, 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, 10, 5, 5, 49, 49, 49, 49, 49, 49, 49] 100 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 166 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942917 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436942917 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942917/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942917/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942917 Building ZINC000436942919 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942919' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942919 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436942919 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942919/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942919 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/747 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@H]1Oc2ccccc2[C@H]1C) `ZINC000436942919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436942919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000436942919 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [24, 6, 24, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 36, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 24, 24, 24, 6, 5, 5, 10, 5, 5, 49, 49, 49, 49, 49, 49, 49] 100 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 165 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942919 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942919/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942919 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/748 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/748' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@H]1Oc2ccccc2[C@H]1C) `ZINC000436942919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436942919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000436942919 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [24, 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, 10, 5, 5, 48, 48, 48, 48, 48, 48, 48] 100 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 163 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942919 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436942919 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942919/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942919/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942919 Building ZINC000436942919 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942919' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942919 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436942919 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942919/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942919 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 747) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@H]1Oc2ccccc2[C@H]1C) `ZINC000436942919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436942919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000436942919 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [24, 6, 24, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 36, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 24, 24, 24, 6, 5, 5, 10, 5, 5, 49, 49, 49, 49, 49, 49, 49] 100 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 165 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942919 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942919/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942919 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 748) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@H]1Oc2ccccc2[C@H]1C) `ZINC000436942919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436942919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000436942919 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [24, 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, 10, 5, 5, 48, 48, 48, 48, 48, 48, 48] 100 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 163 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942919 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436942919 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942919/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942919/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436942919 Building ZINC000436944298 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436944298' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436944298 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436944298 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436944298/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436944298 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/749 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCc1cc(F)ccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436944298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436944298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436944298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436944298 none CSCc1cc(F)ccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)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', '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: [5, 14, 5, 1, 1, 1, 15, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 36, 22, 22, 22, 22, 22, 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, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 187 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436944298 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436944298/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436944298 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/750 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/750' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCc1cc(F)ccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436944298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436944298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436944298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436944298 none CSCc1cc(F)ccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(O)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', '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: [5, 14, 5, 1, 1, 1, 15, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 37, 22, 22, 22, 14, 13, 22, 22, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 37, 37, 22, 22, 22, 13, 13, 3, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 212 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436944298 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436944298 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436944298/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436944298/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436944298 Building ZINC000436944298 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436944298' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436944298 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436944298 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436944298/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436944298 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 749) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CSCc1cc(F)ccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436944298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436944298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436944298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436944298 none CSCc1cc(F)ccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)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', '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: [5, 14, 5, 1, 1, 1, 15, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 36, 22, 22, 22, 22, 22, 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, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 187 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436944298 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436944298/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436944298 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 750) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CSCc1cc(F)ccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436944298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436944298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436944298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000436944298 none CSCc1cc(F)ccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(O)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', '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: [5, 14, 5, 1, 1, 1, 15, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 37, 22, 22, 22, 14, 13, 22, 22, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 37, 37, 22, 22, 22, 13, 13, 3, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 212 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436944298 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436944298 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436944298/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436944298/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436944298 Building ZINC000436945931 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945931' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945931 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436945931 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945931/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945931 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/751 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)c1ccccc1n1cccn1) `ZINC000436945931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436945931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000436945931 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 14, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 14, 30, 30, 16, 30, 30, 30, 48, 48, 48, 48, 14, 14, 14, 6, 4, 4, 8, 4, 4, 30, 30, 30, 30, 48, 48, 48] 100 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: 178 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945931 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945931/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945931 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/752 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/752' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)c1ccccc1n1cccn1) `ZINC000436945931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436945931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000436945931 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 11, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 11, 26, 26, 11, 26, 26, 26, 49, 49, 49, 49, 11, 11, 11, 5, 4, 4, 8, 4, 4, 26, 26, 26, 26, 49, 49, 49] 100 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: 171 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945931 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436945931 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945931/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945931/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945931 Building ZINC000436945931 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945931' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945931 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436945931 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945931/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945931 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 751) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)c1ccccc1n1cccn1) `ZINC000436945931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436945931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000436945931 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 14, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 14, 30, 30, 16, 30, 30, 30, 48, 48, 48, 48, 14, 14, 14, 6, 4, 4, 8, 4, 4, 30, 30, 30, 30, 48, 48, 48] 100 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: 178 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945931 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945931/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945931 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 752) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)c1ccccc1n1cccn1) `ZINC000436945931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436945931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000436945931 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 11, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 11, 26, 26, 11, 26, 26, 26, 49, 49, 49, 49, 11, 11, 11, 5, 4, 4, 8, 4, 4, 26, 26, 26, 26, 49, 49, 49] 100 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: 171 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945931 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436945931 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945931/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945931/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945931 Building ZINC000436945932 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945932' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945932 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436945932 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945932/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945932 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/753 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)c1ccccc1n1cccn1) `ZINC000436945932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436945932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000436945932 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 11, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 11, 26, 26, 11, 26, 26, 26, 50, 50, 50, 50, 11, 11, 11, 5, 4, 4, 8, 4, 4, 26, 26, 26, 26, 50, 50, 50] 100 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: 172 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945932 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945932/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945932 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/754 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/754' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)c1ccccc1n1cccn1) `ZINC000436945932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436945932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000436945932 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 14, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 14, 31, 31, 16, 31, 31, 31, 48, 48, 48, 48, 14, 14, 14, 6, 4, 4, 8, 4, 4, 31, 31, 31, 31, 48, 48, 48] 100 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: 179 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945932 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436945932 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945932/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945932/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945932 Building ZINC000436945932 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945932' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945932 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436945932 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945932/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945932 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 753) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)c1ccccc1n1cccn1) `ZINC000436945932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436945932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000436945932 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 11, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 11, 26, 26, 11, 26, 26, 26, 50, 50, 50, 50, 11, 11, 11, 5, 4, 4, 8, 4, 4, 26, 26, 26, 26, 50, 50, 50] 100 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: 172 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945932 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945932/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945932 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 754) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)c1ccccc1n1cccn1) `ZINC000436945932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436945932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000436945932 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 14, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 14, 31, 31, 16, 31, 31, 31, 48, 48, 48, 48, 14, 14, 14, 6, 4, 4, 8, 4, 4, 31, 31, 31, 31, 48, 48, 48] 100 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: 179 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945932 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436945932 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945932/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945932/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436945932 Building ZINC000436968413 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436968413' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436968413 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436968413 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436968413/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436968413 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/755 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(c2ccccn2)c1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436968413.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436968413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436968413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436968413 none O=C(NCc1cccc(c2ccccn2)c1)[C@@]([O-])([SiH3])c1ccc(O)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', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 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, 3, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 11, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 36, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 11, 11, 38, 38, 38, 50, 50, 50, 50, 38, 2, 2, 4, 2, 2] 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: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436968413 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436968413/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436968413 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/756 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/756' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(c2ccccn2)c1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436968413.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436968413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436968413/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436968413 none O=C(NCc1cccc(c2ccccn2)c1)[C@]([O-])([SiH3])c1ccc(O)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', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 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, 3, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 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, 4, 2, 2] 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: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436968413 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436968413 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436968413/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436968413/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436968413 Building ZINC000436968413 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436968413' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436968413 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436968413 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436968413/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436968413 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 755) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NCc1cccc(c2ccccn2)c1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436968413.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436968413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436968413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436968413 none O=C(NCc1cccc(c2ccccn2)c1)[C@@]([O-])([SiH3])c1ccc(O)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', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 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, 3, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 11, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 36, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 11, 11, 38, 38, 38, 50, 50, 50, 50, 38, 2, 2, 4, 2, 2] 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: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436968413 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436968413/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436968413 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 756) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NCc1cccc(c2ccccn2)c1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436968413.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436968413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436968413/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000436968413 none O=C(NCc1cccc(c2ccccn2)c1)[C@]([O-])([SiH3])c1ccc(O)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', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 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, 3, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 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, 4, 2, 2] 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: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436968413 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436968413 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436968413/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436968413/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436968413 Building ZINC000436969333 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436969333' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436969333 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436969333 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436969333/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436969333 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/757 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(c2n[nH]c(C3CC3)n2)cc1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436969333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436969333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436969333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000436969333 none O=C(Nc1ccc(c2n[nH]c(C3CC3)n2)cc1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 8, 6, 1, 5, 5, 5, 8, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 13, 13, 4, 4, 31, 31, 31, 31, 31, 50, 50, 31, 13, 13, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 13, 13, 50, 50, 50, 50, 50, 13, 13, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/83235/xao-8058115.15/working/building/ZINC000436969333 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436969333/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436969333 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/758 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/758' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(c2n[nH]c(C3CC3)n2)cc1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436969333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436969333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436969333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000436969333 none O=C(Nc1ccc(c2n[nH]c(C3CC3)n2)cc1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 8, 6, 1, 5, 5, 5, 8, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 13, 13, 4, 8, 32, 32, 32, 32, 32, 50, 50, 32, 13, 13, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 13, 13, 50, 50, 50, 50, 50, 13, 13, 4, 4, 8, 4, 4] 100 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436969333 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436969333 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436969333/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436969333/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436969333 Building ZINC000436969333 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436969333' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436969333 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436969333 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436969333/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436969333 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 757) grep: /scratch/xiaobo/83235/xao-8058115.15/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(Nc1ccc(c2n[nH]c(C3CC3)n2)cc1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436969333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436969333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436969333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000436969333 none O=C(Nc1ccc(c2n[nH]c(C3CC3)n2)cc1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 8, 6, 1, 5, 5, 5, 8, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 13, 13, 4, 4, 31, 31, 31, 31, 31, 50, 50, 31, 13, 13, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 13, 13, 50, 50, 50, 50, 50, 13, 13, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/83235/xao-8058115.15/working/building/ZINC000436969333 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436969333/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436969333 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 758) grep: /scratch/xiaobo/83235/xao-8058115.15/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(Nc1ccc(c2n[nH]c(C3CC3)n2)cc1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000436969333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436969333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436969333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000436969333 none O=C(Nc1ccc(c2n[nH]c(C3CC3)n2)cc1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 8, 6, 1, 5, 5, 5, 8, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 13, 13, 4, 8, 32, 32, 32, 32, 32, 50, 50, 32, 13, 13, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 13, 13, 50, 50, 50, 50, 50, 13, 13, 4, 4, 8, 4, 4] 100 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436969333 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436969333 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436969333/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436969333/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436969333 Building ZINC000436960775 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436960775' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436960775 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436960775 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436960775/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436960775 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/759 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C)cc(CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cc1C) `ZINC000436960775.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436960775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436960775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000436960775 none COc1c(C)cc(CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', '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', 'O.3', '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'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 26, 26, 38, 38, 38, 26, 6, 3, 6, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 38, 38, 38, 50, 50, 50, 38, 38, 38, 38, 26, 26, 6, 6, 6, 3, 3, 6, 3, 3, 38, 38, 38, 38] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436960775 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436960775/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436960775 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/760 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/760' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C)cc(CN(C)C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cc1C) `ZINC000436960775.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436960775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436960775/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000436960775 none COc1c(C)cc(CN(C)C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', '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', 'O.3', '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'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 27, 27, 39, 39, 39, 27, 7, 3, 7, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 39, 39, 39, 50, 50, 50, 39, 39, 39, 39, 27, 27, 7, 7, 7, 3, 3, 6, 3, 3, 39, 39, 39, 39] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436960775 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436960775 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436960775/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436960775/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436960775 Building ZINC000436960775 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436960775' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436960775 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436960775 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436960775/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436960775 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 759) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1c(C)cc(CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cc1C) `ZINC000436960775.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436960775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436960775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000436960775 none COc1c(C)cc(CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', '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', 'O.3', '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'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 26, 26, 38, 38, 38, 26, 6, 3, 6, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 38, 38, 38, 50, 50, 50, 38, 38, 38, 38, 26, 26, 6, 6, 6, 3, 3, 6, 3, 3, 38, 38, 38, 38] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436960775 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436960775/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436960775 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 760) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1c(C)cc(CN(C)C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cc1C) `ZINC000436960775.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436960775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436960775/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000436960775 none COc1c(C)cc(CN(C)C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', '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', 'O.3', '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'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 27, 27, 39, 39, 39, 27, 7, 3, 7, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 39, 39, 39, 50, 50, 50, 39, 39, 39, 39, 27, 27, 7, 7, 7, 3, 3, 6, 3, 3, 39, 39, 39, 39] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436960775 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000436960775 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436960775/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436960775/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000436960775 Building ZINC000437003536 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437003536' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437003536 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000437003536 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437003536/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437003536 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/761 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2[nH]c3ccc(F)cc3c2C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000437003536.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000437003536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437003536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000437003536 none O=C(N1CCc2[nH]c3ccc(F)cc3c2C1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 3, 3, 1, 2, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 3, 3, 6, 3, 3] 56 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437003536 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437003536/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437003536 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/762 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/762' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2[nH]c3ccc(F)cc3c2C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000437003536.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000437003536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437003536/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000437003536 none O=C(N1CCc2[nH]c3ccc(F)cc3c2C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 3, 3, 1, 1, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 6, 3, 3] 56 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437003536 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000437003536 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437003536/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437003536/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437003536 Building ZINC000437003536 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437003536' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437003536 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000437003536 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437003536/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437003536 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 761) grep: /scratch/xiaobo/83235/xao-8058115.15/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(N1CCc2[nH]c3ccc(F)cc3c2C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000437003536.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000437003536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437003536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000437003536 none O=C(N1CCc2[nH]c3ccc(F)cc3c2C1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 3, 3, 1, 2, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 3, 3, 6, 3, 3] 56 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437003536 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437003536/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437003536 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 762) grep: /scratch/xiaobo/83235/xao-8058115.15/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(N1CCc2[nH]c3ccc(F)cc3c2C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000437003536.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000437003536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437003536/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000437003536 none O=C(N1CCc2[nH]c3ccc(F)cc3c2C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 3, 3, 1, 1, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 6, 3, 3] 56 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437003536 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000437003536 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437003536/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437003536/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437003536 Building ZINC000437004114 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437004114' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437004114 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000437004114 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437004114/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437004114 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/763 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1csc(c2ccccn2)n1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000437004114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000437004114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437004114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000437004114 none O=C(Nc1csc(c2ccccn2)n1)[C@@]([O-])([SiH3])c1ccc(O)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', 'O.3', 'C.ar', 'C.ar', 'H', '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, 12, 1, 1, 6, 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, 3, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 12, 12, 12, 12, 50, 50, 50, 50, 50, 12, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 12, 50, 50, 50, 50, 5, 5, 10, 5, 5] 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437004114 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437004114/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437004114 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/764 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/764' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1csc(c2ccccn2)n1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000437004114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000437004114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437004114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000437004114 none O=C(Nc1csc(c2ccccn2)n1)[C@]([O-])([SiH3])c1ccc(O)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', 'O.3', 'C.ar', 'C.ar', 'H', '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, 12, 1, 1, 6, 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, 3, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 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, 10, 5, 5] 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437004114 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000437004114 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437004114/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437004114/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437004114 Building ZINC000437004114 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437004114' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437004114 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000437004114 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437004114/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437004114 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 763) grep: /scratch/xiaobo/83235/xao-8058115.15/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(Nc1csc(c2ccccn2)n1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000437004114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000437004114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437004114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000437004114 none O=C(Nc1csc(c2ccccn2)n1)[C@@]([O-])([SiH3])c1ccc(O)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', 'O.3', 'C.ar', 'C.ar', 'H', '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, 12, 1, 1, 6, 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, 3, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 12, 12, 12, 12, 50, 50, 50, 50, 50, 12, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 12, 50, 50, 50, 50, 5, 5, 10, 5, 5] 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437004114 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437004114/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437004114 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 764) grep: /scratch/xiaobo/83235/xao-8058115.15/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(Nc1csc(c2ccccn2)n1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000437004114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000437004114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437004114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000437004114 none O=C(Nc1csc(c2ccccn2)n1)[C@]([O-])([SiH3])c1ccc(O)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', 'O.3', 'C.ar', 'C.ar', 'H', '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, 12, 1, 1, 6, 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, 3, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 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, 10, 5, 5] 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437004114 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000437004114 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437004114/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437004114/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437004114 Building ZINC000437073357 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073357' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073357 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000437073357 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073357/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073357 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/765 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCS1) `ZINC000437073357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000437073357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000437073357 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCS1 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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', '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, 17, 1, 1, 5, 5, 14, 7, 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] 0 hydrogens 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, 21, 21, 21, 21, 10, 2, 10, 1, 1, 1, 4, 4, 1, 4, 4, 4, 21, 21, 21, 44, 44, 44, 44, 44, 21, 21, 4, 4, 4, 4, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073357 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073357/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073357 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/766 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/766' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCS1) `ZINC000437073357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000437073357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000437073357 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCS1 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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', '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, 17, 1, 1, 5, 5, 14, 7, 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] 0 hydrogens 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, 26, 26, 26, 26, 13, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 47, 47, 47, 47, 47, 26, 26, 3, 3, 3, 3, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073357 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000437073357 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073357/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073357/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073357 Building ZINC000437073357 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073357' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073357 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000437073357 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073357/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073357 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 765) grep: /scratch/xiaobo/83235/xao-8058115.15/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@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCS1) `ZINC000437073357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000437073357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000437073357 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCS1 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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', '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, 17, 1, 1, 5, 5, 14, 7, 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] 0 hydrogens 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, 21, 21, 21, 21, 10, 2, 10, 1, 1, 1, 4, 4, 1, 4, 4, 4, 21, 21, 21, 44, 44, 44, 44, 44, 21, 21, 4, 4, 4, 4, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073357 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073357/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073357 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 766) grep: /scratch/xiaobo/83235/xao-8058115.15/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@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCS1) `ZINC000437073357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000437073357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000437073357 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCS1 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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', '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, 17, 1, 1, 5, 5, 14, 7, 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] 0 hydrogens 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, 26, 26, 26, 26, 13, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 47, 47, 47, 47, 47, 26, 26, 3, 3, 3, 3, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073357 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000437073357 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073357/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073357/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073357 Building ZINC000437073366 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073366' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073366 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000437073366 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073366/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073366 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/767 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCS1) `ZINC000437073366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000437073366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000437073366 none CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCS1 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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', '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, 17, 1, 1, 5, 5, 14, 7, 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] 0 hydrogens 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, 11, 2, 11, 1, 1, 1, 3, 3, 1, 3, 3, 3, 24, 24, 24, 46, 46, 46, 46, 46, 24, 24, 3, 3, 3, 3, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073366 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073366/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073366 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/768 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/768' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCS1) `ZINC000437073366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000437073366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000437073366 none CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCS1 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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', '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, 17, 1, 1, 5, 5, 14, 7, 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] 0 hydrogens 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, 21, 21, 21, 21, 11, 2, 11, 1, 1, 1, 4, 4, 1, 1, 4, 4, 21, 21, 21, 45, 45, 45, 45, 45, 21, 21, 4, 4, 4, 4, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073366 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000437073366 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073366/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073366/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073366 Building ZINC000437073366 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073366' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073366 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000437073366 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073366/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073366 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 767) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCS1) `ZINC000437073366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000437073366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000437073366 none CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCS1 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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', '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, 17, 1, 1, 5, 5, 14, 7, 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] 0 hydrogens 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, 11, 2, 11, 1, 1, 1, 3, 3, 1, 3, 3, 3, 24, 24, 24, 46, 46, 46, 46, 46, 24, 24, 3, 3, 3, 3, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073366 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073366/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073366 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 768) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCS1) `ZINC000437073366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000437073366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000437073366 none CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCS1 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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', '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, 17, 1, 1, 5, 5, 14, 7, 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] 0 hydrogens 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, 21, 21, 21, 21, 11, 2, 11, 1, 1, 1, 4, 4, 1, 1, 4, 4, 21, 21, 21, 45, 45, 45, 45, 45, 21, 21, 4, 4, 4, 4, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073366 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000437073366 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073366/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073366/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437073366 Building ZINC000174434625 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434625' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434625 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174434625 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434625/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434625 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/769 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)[C@@H]1c1cccc(F)c1) `ZINC000174434625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174434625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000174434625 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)[C@@H]1c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 77 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434625 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434625/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434625 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/770 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/770' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)[C@@H]1c1cccc(F)c1) `ZINC000174434625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174434625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000174434625 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)[C@@H]1c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 3, 3, 3, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 35, 35, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 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: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434625 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174434625 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434625/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434625/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434625 Building ZINC000174434625 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434625' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434625 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174434625 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434625/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434625 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 769) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)[C@@H]1c1cccc(F)c1) `ZINC000174434625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174434625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000174434625 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)[C@@H]1c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 77 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434625 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434625/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434625 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 770) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)[C@@H]1c1cccc(F)c1) `ZINC000174434625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174434625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000174434625 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)[C@@H]1c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 3, 3, 3, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 35, 35, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 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: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434625 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174434625 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434625/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434625/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434625 Building ZINC000174434641 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434641' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434641 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174434641 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434641/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434641 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/771 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)[C@@H]1c1cccc(F)c1) `ZINC000174434641.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174434641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000174434641 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)[C@@H]1c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 41, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 74 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434641 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434641/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434641 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/772 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/772' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)[C@@H]1c1cccc(F)c1) `ZINC000174434641.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174434641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000174434641 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)[C@@H]1c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 41, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 66 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434641 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174434641 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434641/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434641/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434641 Building ZINC000174434641 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434641' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434641 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174434641 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434641/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434641 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 771) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)[C@@H]1c1cccc(F)c1) `ZINC000174434641.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174434641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000174434641 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)[C@@H]1c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 41, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 74 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434641 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434641/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434641 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 772) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)[C@@H]1c1cccc(F)c1) `ZINC000174434641.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174434641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000174434641 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)[C@@H]1c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 41, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 66 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434641 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174434641 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434641/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434641/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434641 Building ZINC000174434652 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434652' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434652 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174434652 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434652/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434652 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/773 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)[C@H]1c1cccc(F)c1) `ZINC000174434652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174434652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000174434652 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)[C@H]1c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 42, 42, 42, 42, 42, 42, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 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]) total number of confs: 67 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434652 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434652/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434652 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/774 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/774' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)[C@H]1c1cccc(F)c1) `ZINC000174434652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174434652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000174434652 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)[C@H]1c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 41, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 73 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434652 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174434652 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434652/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434652/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434652 Building ZINC000174434652 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434652' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434652 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174434652 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434652/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434652 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 773) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)[C@H]1c1cccc(F)c1) `ZINC000174434652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174434652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000174434652 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)[C@H]1c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 42, 42, 42, 42, 42, 42, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 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]) total number of confs: 67 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434652 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434652/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434652 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 774) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)[C@H]1c1cccc(F)c1) `ZINC000174434652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174434652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000174434652 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)[C@H]1c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 41, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 73 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434652 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174434652 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434652/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434652/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434652 Building ZINC000174434663 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434663' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174434663 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434663/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/775 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)[C@H]1c1cccc(F)c1) `ZINC000174434663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174434663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000174434663 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)[C@H]1c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 3, 3, 3, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 37, 37, 37, 37, 37, 37, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 37, 37, 37, 37] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 63 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434663/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/776 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/776' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)[C@H]1c1cccc(F)c1) `ZINC000174434663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174434663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000174434663 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)[C@H]1c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 77 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174434663 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434663/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434663/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434663 Building ZINC000174434663 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434663' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174434663 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434663/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 775) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)[C@H]1c1cccc(F)c1) `ZINC000174434663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174434663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000174434663 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)[C@H]1c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 3, 3, 3, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 37, 37, 37, 37, 37, 37, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 37, 37, 37, 37] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 63 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434663/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 776) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)[C@H]1c1cccc(F)c1) `ZINC000174434663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174434663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000174434663 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)[C@H]1c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 77 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174434663 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434663/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434663/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174434663 Building ZINC000437722647 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437722647' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437722647 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000437722647 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437722647/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437722647 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/777 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccnc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)c1) `ZINC000437722647.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000437722647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437722647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000437722647 none CCc1ccnc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 26, 26, 26, 26, 26, 12, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 26, 50, 50, 50, 50, 50, 26, 26, 12, 12, 3, 2, 2, 2, 2, 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]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437722647 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437722647/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437722647 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/778 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/778' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccnc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)c1) `ZINC000437722647.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000437722647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437722647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000437722647 none CCc1ccnc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 26, 26, 26, 26, 26, 12, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 26, 50, 50, 50, 50, 50, 26, 26, 12, 12, 3, 2, 2, 2, 2, 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]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437722647 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000437722647 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437722647/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437722647/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437722647 Building ZINC000437722647 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437722647' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437722647 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000437722647 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437722647/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437722647 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 777) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCc1ccnc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)c1) `ZINC000437722647.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000437722647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437722647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000437722647 none CCc1ccnc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 26, 26, 26, 26, 26, 12, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 26, 50, 50, 50, 50, 50, 26, 26, 12, 12, 3, 2, 2, 2, 2, 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]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437722647 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437722647/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437722647 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 778) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCc1ccnc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)c1) `ZINC000437722647.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000437722647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437722647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000437722647 none CCc1ccnc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 26, 26, 26, 26, 26, 12, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 26, 50, 50, 50, 50, 50, 26, 26, 12, 12, 3, 2, 2, 2, 2, 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]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437722647 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000437722647 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437722647/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437722647/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000437722647 Building ZINC000438383095 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383095' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383095 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438383095 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383095/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383095 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/779 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@@H](C)[C@H]2C)cc1Cl) `ZINC000438383095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438383095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438383095 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@@H](C)[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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 2, 8, 8, 1, 1, 1, 2, 9, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 16, 16, 16, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383095 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383095/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383095 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/780 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/780' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@@H](C)[C@H]2C)cc1Cl) `ZINC000438383095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438383095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438383095 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@@H](C)[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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 2, 6, 6, 1, 1, 1, 2, 10, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 11, 11, 11, 6, 6, 15, 15, 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, 39, 40, 41]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383095 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438383095 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383095/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383095/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383095 Building ZINC000438383095 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383095' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383095 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438383095 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383095/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383095 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 779) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@@H](C)[C@H]2C)cc1Cl) `ZINC000438383095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438383095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438383095 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@@H](C)[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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 2, 8, 8, 1, 1, 1, 2, 9, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 16, 16, 16, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383095 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383095/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383095 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 780) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@@H](C)[C@H]2C)cc1Cl) `ZINC000438383095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438383095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438383095 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@@H](C)[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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 2, 6, 6, 1, 1, 1, 2, 10, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 11, 11, 11, 6, 6, 15, 15, 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, 39, 40, 41]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383095 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438383095 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383095/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383095/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383095 Building ZINC000438383096 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383096' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383096 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438383096 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383096/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383096 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/781 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@@H](C)[C@@H]2C)cc1Cl) `ZINC000438383096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438383096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438383096 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@@H](C)[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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 2, 10, 10, 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, 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, 39, 40, 41]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383096 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383096/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383096 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/782 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/782' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@@H](C)[C@@H]2C)cc1Cl) `ZINC000438383096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438383096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438383096 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@@H](C)[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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 4, 8, 8, 1, 1, 1, 2, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 8, 15, 15, 15, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 61 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383096 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438383096 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383096/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383096/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383096 Building ZINC000438383096 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383096' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383096 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438383096 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383096/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383096 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 781) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@@H](C)[C@@H]2C)cc1Cl) `ZINC000438383096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438383096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438383096 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@@H](C)[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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 2, 10, 10, 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, 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, 39, 40, 41]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383096 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383096/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383096 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 782) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@@H](C)[C@@H]2C)cc1Cl) `ZINC000438383096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438383096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438383096 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@@H](C)[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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 4, 8, 8, 1, 1, 1, 2, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 8, 15, 15, 15, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 61 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383096 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438383096 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383096/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383096/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383096 Building ZINC000438383097 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383097' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383097 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438383097 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383097/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383097 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/783 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@H](C)[C@@H]2C)cc1Cl) `ZINC000438383097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438383097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438383097 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@H](C)[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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 14, 14, 14, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383097 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383097/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383097 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/784 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/784' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@H](C)[C@@H]2C)cc1Cl) `ZINC000438383097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438383097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438383097 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@H](C)[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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 12, 1, 12, 12, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 69 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383097 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438383097 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383097/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383097/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383097 Building ZINC000438383097 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383097' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383097 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438383097 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383097/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383097 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 783) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@H](C)[C@@H]2C)cc1Cl) `ZINC000438383097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438383097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438383097 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@H](C)[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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 14, 14, 14, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383097 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383097/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383097 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 784) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@H](C)[C@@H]2C)cc1Cl) `ZINC000438383097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438383097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438383097 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@H](C)[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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 12, 1, 12, 12, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 69 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383097 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438383097 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383097/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383097/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383097 Building ZINC000438383098 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383098' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383098 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438383098 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383098/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383098 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/785 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@H](C)[C@H]2C)cc1Cl) `ZINC000438383098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438383098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438383098 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@H](C)[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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 10, 10, 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, 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, 39, 40, 41]) total number of confs: 66 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383098 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383098/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383098 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/786 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/786' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@H](C)[C@H]2C)cc1Cl) `ZINC000438383098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438383098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438383098 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@H](C)[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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 6, 12, 12, 12, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 61 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383098 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438383098 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383098/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383098/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383098 Building ZINC000438383098 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383098' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383098 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438383098 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383098/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383098 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 785) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@H](C)[C@H]2C)cc1Cl) `ZINC000438383098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438383098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438383098 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@H](C)[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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 10, 10, 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, 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, 39, 40, 41]) total number of confs: 66 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383098 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383098/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383098 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 786) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@H](C)[C@H]2C)cc1Cl) `ZINC000438383098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438383098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438383098 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@H](C)[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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 6, 12, 12, 12, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 61 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383098 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438383098 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383098/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383098/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438383098 Building ZINC000438393964 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393964' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393964 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438393964 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393964/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393964 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/787 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/787' -> `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(Br)cc2)[C@H](C)[C@@H](C)O1) `ZINC000438393964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438393964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000438393964 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)[C@@H](C)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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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, 17, 1, 1, 5, 7, 5, 5, 7, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 9, 1, 9, 1, 1, 1, 4, 4, 1, 1, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 19, 19, 19, 19, 19, 19] 24 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: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393964 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393964/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393964 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/788 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/788' -> `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(Br)cc2)[C@H](C)[C@@H](C)O1) `ZINC000438393964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438393964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000438393964 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)[C@@H](C)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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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, 17, 1, 1, 5, 7, 5, 5, 7, 5, 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, 3, 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: [17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17] 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, 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/83235/xao-8058115.15/working/building/ZINC000438393964 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438393964 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393964/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393964/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393964 Building ZINC000438393964 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393964' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393964 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438393964 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393964/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393964 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 787) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)[C@@H](C)O1) `ZINC000438393964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438393964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000438393964 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)[C@@H](C)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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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, 17, 1, 1, 5, 7, 5, 5, 7, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 9, 1, 9, 1, 1, 1, 4, 4, 1, 1, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 19, 19, 19, 19, 19, 19] 24 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: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393964 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393964/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393964 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 788) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)[C@@H](C)O1) `ZINC000438393964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438393964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000438393964 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)[C@@H](C)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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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, 17, 1, 1, 5, 7, 5, 5, 7, 5, 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, 3, 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: [17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17] 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, 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/83235/xao-8058115.15/working/building/ZINC000438393964 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438393964 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393964/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393964/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393964 Building ZINC000438393966 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393966' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393966 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438393966 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393966/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393966 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/789 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/789' -> `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(Br)cc2)[C@H](C)[C@H](C)O1) `ZINC000438393966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438393966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000438393966 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)[C@H](C)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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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, 17, 1, 1, 5, 7, 5, 5, 7, 5, 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, 3, 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: [15, 15, 15, 15, 7, 2, 7, 1, 1, 1, 5, 5, 2, 2, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15] 18 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]) total number of confs: 39 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393966 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393966/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393966 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/790 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/790' -> `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(Br)cc2)[C@H](C)[C@H](C)O1) `ZINC000438393966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438393966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000438393966 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)[C@H](C)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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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, 17, 1, 1, 5, 7, 5, 5, 7, 5, 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, 3, 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, 11, 11, 7, 2, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11] 11 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]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393966 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438393966 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393966/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393966/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393966 Building ZINC000438393966 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393966' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393966 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438393966 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393966/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393966 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 789) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)[C@H](C)O1) `ZINC000438393966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438393966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000438393966 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)[C@H](C)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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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, 17, 1, 1, 5, 7, 5, 5, 7, 5, 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, 3, 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: [15, 15, 15, 15, 7, 2, 7, 1, 1, 1, 5, 5, 2, 2, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15] 18 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]) total number of confs: 39 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393966 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393966/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393966 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 790) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)[C@H](C)O1) `ZINC000438393966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438393966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000438393966 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)[C@H](C)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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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, 17, 1, 1, 5, 7, 5, 5, 7, 5, 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, 3, 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, 11, 11, 7, 2, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11] 11 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]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393966 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438393966 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393966/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393966/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393966 Building ZINC000438393968 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393968' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393968 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438393968 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393968/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393968 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/791 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/791' -> `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(Br)cc2)[C@@H](C)[C@@H](C)O1) `ZINC000438393968.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438393968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000438393968 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)[C@@H](C)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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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, 17, 1, 1, 5, 7, 5, 5, 7, 5, 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, 3, 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: [21, 21, 21, 21, 15, 2, 15, 1, 1, 1, 4, 4, 1, 4, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 4, 21, 21, 21, 21, 21, 21] 26 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393968 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393968/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393968 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/792 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/792' -> `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(Br)cc2)[C@@H](C)[C@@H](C)O1) `ZINC000438393968.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438393968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393968/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000438393968 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)[C@@H](C)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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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, 17, 1, 1, 5, 7, 5, 5, 7, 5, 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, 3, 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: [30, 30, 30, 30, 17, 2, 17, 1, 1, 1, 4, 4, 1, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30] 36 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 71 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393968 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438393968 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393968/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393968/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393968 Building ZINC000438393968 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393968' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393968 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438393968 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393968/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393968 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 791) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)[C@@H](C)O1) `ZINC000438393968.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438393968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000438393968 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)[C@@H](C)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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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, 17, 1, 1, 5, 7, 5, 5, 7, 5, 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, 3, 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: [21, 21, 21, 21, 15, 2, 15, 1, 1, 1, 4, 4, 1, 4, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 4, 21, 21, 21, 21, 21, 21] 26 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393968 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393968/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393968 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 792) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)[C@@H](C)O1) `ZINC000438393968.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438393968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393968/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000438393968 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)[C@@H](C)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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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, 17, 1, 1, 5, 7, 5, 5, 7, 5, 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, 3, 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: [30, 30, 30, 30, 17, 2, 17, 1, 1, 1, 4, 4, 1, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30] 36 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 71 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393968 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438393968 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393968/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393968/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393968 Building ZINC000438393970 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393970' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393970 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438393970 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393970/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393970 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/793 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/793' -> `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(Br)cc2)[C@@H](C)[C@H](C)O1) `ZINC000438393970.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438393970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000438393970 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)[C@H](C)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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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, 17, 1, 1, 5, 7, 5, 5, 7, 5, 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, 3, 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: [26, 26, 26, 26, 17, 2, 17, 1, 1, 1, 6, 6, 1, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26] 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]) total number of confs: 72 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393970 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393970/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393970 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/794 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/794' -> `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(Br)cc2)[C@@H](C)[C@H](C)O1) `ZINC000438393970.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438393970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000438393970 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)[C@H](C)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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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, 17, 1, 1, 5, 7, 5, 5, 7, 5, 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, 3, 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, 35, 35, 35, 19, 3, 19, 1, 1, 1, 5, 5, 1, 1, 5, 5, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 5, 5, 5, 5, 35, 35, 35, 35, 35, 35] 41 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 79 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393970 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438393970 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393970/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393970/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393970 Building ZINC000438393970 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393970' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393970 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438393970 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393970/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393970 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 793) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)[C@H](C)O1) `ZINC000438393970.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438393970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000438393970 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)[C@H](C)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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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, 17, 1, 1, 5, 7, 5, 5, 7, 5, 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, 3, 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: [26, 26, 26, 26, 17, 2, 17, 1, 1, 1, 6, 6, 1, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26] 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]) total number of confs: 72 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393970 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393970/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393970 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 794) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)[C@H](C)O1) `ZINC000438393970.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438393970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000438393970 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)[C@H](C)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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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, 17, 1, 1, 5, 7, 5, 5, 7, 5, 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, 3, 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, 35, 35, 35, 19, 3, 19, 1, 1, 1, 5, 5, 1, 1, 5, 5, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 5, 5, 5, 5, 35, 35, 35, 35, 35, 35] 41 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 79 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393970 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438393970 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393970/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393970/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438393970 Building ZINC000438488102 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438488102' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438488102 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438488102 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438488102/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438488102 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/795 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1nnc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cn21) `ZINC000438488102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438488102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438488102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000438488102 none CC(C)c1nnc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cn21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.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.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 25, 25, 25, 25, 25, 25, 5, 5, 1, 5, 1, 1, 1, 4, 4, 2, 2, 4, 4, 25, 25, 50, 50, 50, 50, 50, 50, 50, 25, 25, 5, 4, 4, 4, 4, 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]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438488102 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438488102/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438488102 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/796 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/796' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1nnc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cn21) `ZINC000438488102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438488102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438488102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000438488102 none CC(C)c1nnc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cn21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.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.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 26, 26, 26, 26, 26, 26, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 26, 26, 50, 50, 50, 50, 50, 50, 50, 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, 36, 37, 38]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438488102 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438488102 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438488102/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438488102/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438488102 Building ZINC000438488102 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438488102' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438488102 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438488102 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438488102/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438488102 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 795) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/795: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1nnc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cn21) `ZINC000438488102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438488102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438488102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000438488102 none CC(C)c1nnc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cn21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.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.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 25, 25, 25, 25, 25, 25, 5, 5, 1, 5, 1, 1, 1, 4, 4, 2, 2, 4, 4, 25, 25, 50, 50, 50, 50, 50, 50, 50, 25, 25, 5, 4, 4, 4, 4, 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]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438488102 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438488102/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438488102 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 796) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/796: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1nnc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cn21) `ZINC000438488102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438488102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438488102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000438488102 none CC(C)c1nnc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cn21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.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.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 26, 26, 26, 26, 26, 26, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 26, 26, 50, 50, 50, 50, 50, 50, 50, 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, 36, 37, 38]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438488102 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438488102 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438488102/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438488102/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438488102 Building ZINC000438489854 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489854' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489854 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438489854 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489854/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489854 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/797 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCC[C@@](O)(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000438489854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438489854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000438489854 none CC1(C)CCC[C@@](O)(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 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, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 27, 27, 16, 27, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 81, 15, 15, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489854 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489854/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489854 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/798 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/798' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCC[C@@](O)(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000438489854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438489854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000438489854 none CC1(C)CCC[C@@](O)(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 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, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 31, 31, 15, 31, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 93, 14, 14, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 196 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489854 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438489854 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489854/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489854/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489854 Building ZINC000438489854 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489854' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489854 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438489854 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489854/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489854 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 797) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC1(C)CCC[C@@](O)(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000438489854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438489854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000438489854 none CC1(C)CCC[C@@](O)(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 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, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 27, 27, 16, 27, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 81, 15, 15, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489854 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489854/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489854 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 798) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC1(C)CCC[C@@](O)(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000438489854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438489854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000438489854 none CC1(C)CCC[C@@](O)(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 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, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 31, 31, 15, 31, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 93, 14, 14, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 196 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489854 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438489854 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489854/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489854/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489854 Building ZINC000438489855 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489855' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489855 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438489855 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489855/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489855 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/799 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCC[C@](O)(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000438489855.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438489855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000438489855 none CC1(C)CCC[C@](O)(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 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, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 30, 30, 17, 30, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 90, 14, 14, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 187 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489855 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489855/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489855 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/800 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/800' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCC[C@](O)(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000438489855.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438489855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489855/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000438489855 none CC1(C)CCC[C@](O)(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 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, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 30, 30, 15, 30, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 90, 14, 14, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 195 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489855 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438489855 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489855/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489855/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489855 Building ZINC000438489855 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489855' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489855 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438489855 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489855/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489855 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 799) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC1(C)CCC[C@](O)(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000438489855.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438489855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000438489855 none CC1(C)CCC[C@](O)(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 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, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 30, 30, 17, 30, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 90, 14, 14, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 187 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489855 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489855/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489855 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 800) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC1(C)CCC[C@](O)(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000438489855.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438489855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489855/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000438489855 none CC1(C)CCC[C@](O)(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 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, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 30, 30, 15, 30, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 90, 14, 14, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 195 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489855 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438489855 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489855/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489855/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438489855 Building ZINC000438616453 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616453' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616453 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438616453 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616453/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616453 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/801 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/801' -> `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)c2ccncc2OC)cc1Cl) `ZINC000438616453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438616453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438616453 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccncc2OC)cc1Cl NO_LONG_NAME dock atom 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.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 8, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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: [14, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 11, 11, 10, 11, 11, 11, 16, 6, 6, 6, 14, 14, 14, 6, 6, 4, 6, 6, 6, 11, 11, 11, 16, 16, 16, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 75 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616453 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616453/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616453 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/802 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/802' -> `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)c2ccncc2OC)cc1Cl) `ZINC000438616453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438616453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438616453 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccncc2OC)cc1Cl NO_LONG_NAME dock atom 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.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 8, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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: [16, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 12, 12, 11, 12, 12, 12, 18, 6, 6, 6, 16, 16, 16, 6, 6, 4, 7, 7, 7, 12, 12, 12, 18, 18, 18, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 85 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616453 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438616453 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616453/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616453/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616453 Building ZINC000438616453 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616453' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616453 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438616453 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616453/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616453 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 801) grep: /scratch/xiaobo/83235/xao-8058115.15/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@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccncc2OC)cc1Cl) `ZINC000438616453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438616453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438616453 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccncc2OC)cc1Cl NO_LONG_NAME dock atom 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.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 8, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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: [14, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 11, 11, 10, 11, 11, 11, 16, 6, 6, 6, 14, 14, 14, 6, 6, 4, 6, 6, 6, 11, 11, 11, 16, 16, 16, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 75 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616453 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616453/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616453 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 802) grep: /scratch/xiaobo/83235/xao-8058115.15/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@@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccncc2OC)cc1Cl) `ZINC000438616453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438616453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438616453 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccncc2OC)cc1Cl NO_LONG_NAME dock atom 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.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 8, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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: [16, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 12, 12, 11, 12, 12, 12, 18, 6, 6, 6, 16, 16, 16, 6, 6, 4, 7, 7, 7, 12, 12, 12, 18, 18, 18, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 85 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616453 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438616453 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616453/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616453/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616453 Building ZINC000438616454 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616454' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616454 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438616454 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616454/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616454 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/803 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/803' -> `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)c2ccncc2OC)cc1Cl) `ZINC000438616454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438616454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438616454 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2ccncc2OC)cc1Cl NO_LONG_NAME dock atom 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.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 8, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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: [15, 6, 4, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 12, 12, 12, 12, 12, 12, 17, 6, 6, 6, 15, 15, 15, 6, 6, 4, 7, 7, 7, 12, 12, 12, 17, 17, 17, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 76 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616454 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616454/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616454 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/804 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/804' -> `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)c2ccncc2OC)cc1Cl) `ZINC000438616454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438616454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438616454 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2ccncc2OC)cc1Cl NO_LONG_NAME dock atom 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.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 8, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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: [15, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 11, 11, 11, 11, 11, 11, 16, 6, 6, 6, 15, 15, 15, 6, 6, 4, 6, 6, 6, 11, 11, 11, 16, 16, 16, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 73 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616454 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438616454 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616454/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616454/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616454 Building ZINC000438616454 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616454' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616454 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438616454 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616454/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616454 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 803) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2ccncc2OC)cc1Cl) `ZINC000438616454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438616454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438616454 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2ccncc2OC)cc1Cl NO_LONG_NAME dock atom 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.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 8, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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: [15, 6, 4, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 12, 12, 12, 12, 12, 12, 17, 6, 6, 6, 15, 15, 15, 6, 6, 4, 7, 7, 7, 12, 12, 12, 17, 17, 17, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 76 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616454 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616454/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616454 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 804) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2ccncc2OC)cc1Cl) `ZINC000438616454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438616454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438616454 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2ccncc2OC)cc1Cl NO_LONG_NAME dock atom 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.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 8, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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: [15, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 11, 11, 11, 11, 11, 11, 16, 6, 6, 6, 15, 15, 15, 6, 6, 4, 6, 6, 6, 11, 11, 11, 16, 16, 16, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 73 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616454 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438616454 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616454/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616454/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438616454 Building ZINC000337328585 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337328585' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337328585 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337328585 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337328585/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337328585 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/805 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(F)cc2c1CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CC2) `ZINC000337328585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337328585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337328585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000337328585 none Cc1cc(F)cc2c1CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CC2 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.2', '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'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 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] 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] 0 hydrogens 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, 7, 2, 9, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 19, 19, 19, 19] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337328585 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337328585/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337328585 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/806 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/806' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(F)cc2c1CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CC2) `ZINC000337328585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337328585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337328585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000337328585 none Cc1cc(F)cc2c1CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CC2 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.2', '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'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 2, 9, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 17, 17, 17, 17] 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: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337328585 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337328585 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337328585/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337328585/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337328585 Building ZINC000337328585 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337328585' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337328585 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337328585 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337328585/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337328585 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 805) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1cc(F)cc2c1CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CC2) `ZINC000337328585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337328585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337328585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000337328585 none Cc1cc(F)cc2c1CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CC2 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.2', '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'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 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] 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] 0 hydrogens 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, 7, 2, 9, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 19, 19, 19, 19] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337328585 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337328585/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337328585 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 806) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1cc(F)cc2c1CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CC2) `ZINC000337328585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337328585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337328585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000337328585 none Cc1cc(F)cc2c1CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CC2 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.2', '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'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 2, 9, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 17, 17, 17, 17] 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: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337328585 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337328585 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337328585/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337328585/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337328585 Building ZINC000438911190 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438911190' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438911190 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438911190 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438911190/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438911190 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/807 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)nc2cc(Cl)ccc21) `ZINC000438911190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438911190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438911190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438911190 none Cn1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 8, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 6, 6, 12, 6, 6, 12, 12, 12] 24 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]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438911190 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438911190/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438911190 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/808 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/808' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)nc2cc(Cl)ccc21) `ZINC000438911190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438911190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438911190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438911190 none Cn1c(NC(=O)[C@]([O-])([SiH3])c2ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [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, 12, 6, 6, 11, 11, 11] 22 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]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438911190 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438911190 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438911190/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438911190/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438911190 Building ZINC000438911190 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438911190' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438911190 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438911190 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438911190/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438911190 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 807) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cn1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)nc2cc(Cl)ccc21) `ZINC000438911190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438911190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438911190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438911190 none Cn1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 8, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 6, 6, 12, 6, 6, 12, 12, 12] 24 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]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438911190 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438911190/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438911190 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 808) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cn1c(NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)nc2cc(Cl)ccc21) `ZINC000438911190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438911190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438911190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000438911190 none Cn1c(NC(=O)[C@]([O-])([SiH3])c2ccc(O)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', 'O.3', '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', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [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, 12, 6, 6, 11, 11, 11] 22 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]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438911190 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000438911190 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438911190/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438911190/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000438911190 Building ZINC000439140663 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439140663' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439140663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439140663 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439140663/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439140663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/809 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CC2) `ZINC000439140663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439140663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439140663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000439140663 none COc1ccc2c(c1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)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', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 7, 7, 7, 7, 7, 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, 35, 35, 35, 35, 35, 35, 35, 35, 35, 9, 2, 12, 1, 1, 1, 4, 4, 1, 2, 4, 4, 35, 35, 50, 50, 50, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4, 35, 35, 35, 35] 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: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439140663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439140663/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439140663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/810 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/810' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CC2) `ZINC000439140663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439140663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439140663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000439140663 none COc1ccc2c(c1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)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', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 7, 7, 7, 7, 7, 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, 37, 37, 37, 37, 37, 37, 37, 37, 37, 9, 2, 12, 1, 1, 1, 3, 3, 1, 1, 3, 3, 37, 37, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 3, 3, 3, 3, 37, 37, 37, 37] 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: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439140663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439140663 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439140663/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439140663/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439140663 Building ZINC000439140663 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439140663' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439140663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439140663 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439140663/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439140663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 809) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc2c(c1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CC2) `ZINC000439140663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439140663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439140663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000439140663 none COc1ccc2c(c1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)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', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 7, 7, 7, 7, 7, 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, 35, 35, 35, 35, 35, 35, 35, 35, 35, 9, 2, 12, 1, 1, 1, 4, 4, 1, 2, 4, 4, 35, 35, 50, 50, 50, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4, 35, 35, 35, 35] 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: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439140663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439140663/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439140663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 810) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc2c(c1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CC2) `ZINC000439140663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439140663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439140663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000439140663 none COc1ccc2c(c1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)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', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 7, 7, 7, 7, 7, 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, 37, 37, 37, 37, 37, 37, 37, 37, 37, 9, 2, 12, 1, 1, 1, 3, 3, 1, 1, 3, 3, 37, 37, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 3, 3, 3, 3, 37, 37, 37, 37] 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: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439140663 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439140663 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439140663/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439140663/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439140663 Building ZINC000439238334 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439238334' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439238334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439238334 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439238334/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439238334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/811 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1cccnc1C) `ZINC000439238334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439238334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439238334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000439238334 none CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1cccnc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 12, 20, 20, 20, 20, 20, 20, 14, 14, 14, 14, 14, 6, 13, 13, 6, 13, 13, 6, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 90 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439238334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439238334/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439238334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/812 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/812' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1cccnc1C) `ZINC000439238334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439238334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439238334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000439238334 none CCN(C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1cccnc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 13, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 13, 21, 21, 21, 21, 21, 21, 15, 15, 15, 15, 15, 6, 13, 13, 6, 13, 13, 6, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 91 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439238334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439238334 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439238334/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439238334/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439238334 Building ZINC000439238334 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439238334' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439238334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439238334 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439238334/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439238334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 811) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1cccnc1C) `ZINC000439238334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439238334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439238334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000439238334 none CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1cccnc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 12, 20, 20, 20, 20, 20, 20, 14, 14, 14, 14, 14, 6, 13, 13, 6, 13, 13, 6, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 90 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439238334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439238334/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439238334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 812) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCN(C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1cccnc1C) `ZINC000439238334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439238334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439238334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000439238334 none CCN(C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1cccnc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 13, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 13, 21, 21, 21, 21, 21, 21, 15, 15, 15, 15, 15, 6, 13, 13, 6, 13, 13, 6, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 91 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439238334 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439238334 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439238334/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439238334/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439238334 Building ZINC000439500948 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500948' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500948 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439500948 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500948/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500948 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/813 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000439500948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439500948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000439500948 none CC[C@@H](C)[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 38, 43, 45, 19, 40, 41, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 46, 46, 46, 46, 46, 46, 45, 46, 41, 41, 41, 123, 19, 19, 4, 3, 3, 3, 3] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 348 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500948 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500948/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500948 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/814 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/814' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000439500948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439500948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000439500948 none CC[C@@H](C)[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 38, 43, 46, 20, 39, 41, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 41, 41, 41, 123, 20, 20, 4, 3, 3, 3, 3] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 353 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500948 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439500948 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500948/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500948/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500948 Building ZINC000439500948 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500948' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500948 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439500948 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500948/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500948 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 813) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/813: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000439500948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439500948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000439500948 none CC[C@@H](C)[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 38, 43, 45, 19, 40, 41, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 46, 46, 46, 46, 46, 46, 45, 46, 41, 41, 41, 123, 19, 19, 4, 3, 3, 3, 3] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 348 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500948 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500948/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500948 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 814) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/814: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000439500948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439500948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000439500948 none CC[C@@H](C)[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 38, 43, 46, 20, 39, 41, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 41, 41, 41, 123, 20, 20, 4, 3, 3, 3, 3] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 353 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500948 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439500948 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500948/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500948/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500948 Building ZINC000439500953 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500953' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500953 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439500953 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500953/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500953 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/815 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000439500953.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439500953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000439500953 none CC[C@H](C)[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 38, 43, 46, 20, 39, 41, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 41, 41, 41, 123, 20, 20, 4, 3, 3, 3, 3] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 356 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500953 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500953/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500953 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/816 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/816' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000439500953.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439500953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000439500953 none CC[C@H](C)[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 38, 43, 45, 19, 40, 41, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 46, 46, 46, 46, 46, 46, 46, 45, 41, 41, 41, 123, 19, 19, 4, 3, 3, 3, 3] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 347 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500953 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439500953 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500953/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500953/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500953 Building ZINC000439500953 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500953' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500953 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439500953 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500953/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500953 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 815) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/815: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000439500953.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439500953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000439500953 none CC[C@H](C)[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 38, 43, 46, 20, 39, 41, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 41, 41, 41, 123, 20, 20, 4, 3, 3, 3, 3] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 356 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500953 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500953/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500953 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 816) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/816: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000439500953.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439500953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000439500953 none CC[C@H](C)[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 38, 43, 45, 19, 40, 41, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 46, 46, 46, 46, 46, 46, 46, 45, 41, 41, 41, 123, 19, 19, 4, 3, 3, 3, 3] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 347 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500953 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439500953 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500953/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500953/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439500953 Building ZINC000439858275 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000439858275 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/817 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@H]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1) `ZINC000439858275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439858275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000439858275 none Cc1noc([C@H]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 8, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 13, 13, 13, 13, 13, 7, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 50, 50, 50, 50, 13, 13, 13, 13, 4, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 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, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/818 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/818' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@H]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1) `ZINC000439858275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439858275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000439858275 none Cc1noc([C@H]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 8, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 13, 13, 13, 13, 13, 7, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 50, 50, 50, 50, 13, 13, 13, 13, 4, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 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, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/819 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/819' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1) `ZINC000439858275.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000439858275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000439858275 none Cc1noc([C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 8, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 13, 13, 13, 13, 13, 7, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 50, 50, 50, 50, 13, 13, 13, 13, 4, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 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, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/820 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/820' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1) `ZINC000439858275.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000439858275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000439858275 none Cc1noc([C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 8, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 13, 13, 13, 13, 13, 7, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 50, 50, 50, 50, 13, 13, 13, 13, 4, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 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, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439858275 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 Building ZINC000439858275 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000439858275 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 817) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1noc([C@H]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1) `ZINC000439858275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439858275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000439858275 none Cc1noc([C@H]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 8, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 13, 13, 13, 13, 13, 7, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 50, 50, 50, 50, 13, 13, 13, 13, 4, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 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, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 818) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1noc([C@H]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1) `ZINC000439858275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439858275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000439858275 none Cc1noc([C@H]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 8, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 13, 13, 13, 13, 13, 7, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 50, 50, 50, 50, 13, 13, 13, 13, 4, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 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, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 819) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/819: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1) `ZINC000439858275.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000439858275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000439858275 none Cc1noc([C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 8, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 13, 13, 13, 13, 13, 7, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 50, 50, 50, 50, 13, 13, 13, 13, 4, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 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, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 820) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/820: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1) `ZINC000439858275.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000439858275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000439858275 none Cc1noc([C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 8, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 13, 13, 13, 13, 13, 7, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 50, 50, 50, 50, 13, 13, 13, 13, 4, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 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, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439858275 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 Building ZINC000439858275 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000439858275 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 817) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1noc([C@H]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1) `ZINC000439858275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439858275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000439858275 none Cc1noc([C@H]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 8, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 13, 13, 13, 13, 13, 7, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 50, 50, 50, 50, 13, 13, 13, 13, 4, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 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, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 818) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1noc([C@H]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1) `ZINC000439858275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439858275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000439858275 none Cc1noc([C@H]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 8, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 13, 13, 13, 13, 13, 7, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 50, 50, 50, 50, 13, 13, 13, 13, 4, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 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, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 819) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/819: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1) `ZINC000439858275.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000439858275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000439858275 none Cc1noc([C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 8, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 13, 13, 13, 13, 13, 7, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 50, 50, 50, 50, 13, 13, 13, 13, 4, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 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, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 820) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/820: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1) `ZINC000439858275.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000439858275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000439858275 none Cc1noc([C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 8, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 13, 13, 13, 13, 13, 7, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 50, 50, 50, 50, 13, 13, 13, 13, 4, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 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, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439858275 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 Building ZINC000439858275 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000439858275 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 817) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1noc([C@H]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1) `ZINC000439858275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439858275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000439858275 none Cc1noc([C@H]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 8, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 13, 13, 13, 13, 13, 7, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 50, 50, 50, 50, 13, 13, 13, 13, 4, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 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, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 818) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1noc([C@H]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1) `ZINC000439858275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439858275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000439858275 none Cc1noc([C@H]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 8, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 13, 13, 13, 13, 13, 7, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 50, 50, 50, 50, 13, 13, 13, 13, 4, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 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, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 819) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/819: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1) `ZINC000439858275.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000439858275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000439858275 none Cc1noc([C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 8, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 13, 13, 13, 13, 13, 7, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 50, 50, 50, 50, 13, 13, 13, 13, 4, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 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, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 820) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/820: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1) `ZINC000439858275.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000439858275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000439858275 none Cc1noc([C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 8, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 13, 13, 13, 13, 13, 7, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 50, 50, 50, 50, 13, 13, 13, 13, 4, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 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, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439858275 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439858275 Building ZINC000439910391 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910391' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910391 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439910391 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910391/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910391 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/821 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]([C@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000439910391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439910391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000439910391 none O=C(N1CCC[C@@H]([C@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 6, 11, 11, 11, 11, 11, 13, 29, 29, 29, 29, 29, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 29, 29, 29, 29, 29, 29, 11, 11, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 80 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910391 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910391/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910391 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/822 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/822' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]([C@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000439910391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439910391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000439910391 none O=C(N1CCC[C@@H]([C@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 8, 15, 15, 15, 15, 15, 18, 27, 27, 27, 27, 27, 15, 1, 1, 1, 6, 6, 9, 9, 6, 9, 9, 9, 15, 15, 15, 15, 15, 15, 27, 27, 27, 27, 27, 27, 15, 15, 6, 9, 9, 9, 9, 9, 9, 9, 9] 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: 88 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910391 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439910391 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910391/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910391/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910391 Building ZINC000439910391 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910391' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910391 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439910391 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910391/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910391 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 821) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCC[C@@H]([C@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000439910391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439910391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000439910391 none O=C(N1CCC[C@@H]([C@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 6, 11, 11, 11, 11, 11, 13, 29, 29, 29, 29, 29, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 29, 29, 29, 29, 29, 29, 11, 11, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 80 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910391 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910391/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910391 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 822) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCC[C@@H]([C@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000439910391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439910391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000439910391 none O=C(N1CCC[C@@H]([C@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 8, 15, 15, 15, 15, 15, 18, 27, 27, 27, 27, 27, 15, 1, 1, 1, 6, 6, 9, 9, 6, 9, 9, 9, 15, 15, 15, 15, 15, 15, 27, 27, 27, 27, 27, 27, 15, 15, 6, 9, 9, 9, 9, 9, 9, 9, 9] 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: 88 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910391 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439910391 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910391/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910391/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910391 Building ZINC000439910392 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910392' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910392 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439910392 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910392/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910392 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/823 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]([C@@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000439910392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439910392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000439910392 none O=C(N1CCC[C@@H]([C@@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 7, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 12, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 12, 12, 5, 5, 5, 5, 5, 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, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 74 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910392 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910392/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910392 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/824 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/824' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]([C@@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000439910392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439910392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000439910392 none O=C(N1CCC[C@@H]([C@@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 15, 15, 15, 15, 15, 18, 25, 25, 25, 25, 25, 15, 1, 1, 1, 6, 6, 11, 11, 6, 11, 11, 11, 15, 15, 15, 15, 15, 15, 25, 25, 25, 25, 25, 25, 15, 15, 6, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 98 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910392 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439910392 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910392/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910392/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910392 Building ZINC000439910392 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910392' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910392 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439910392 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910392/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910392 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 823) grep: /scratch/xiaobo/83235/xao-8058115.15/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]([C@@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000439910392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439910392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000439910392 none O=C(N1CCC[C@@H]([C@@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 7, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 12, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 12, 12, 5, 5, 5, 5, 5, 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, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 74 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910392 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910392/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910392 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 824) grep: /scratch/xiaobo/83235/xao-8058115.15/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]([C@@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000439910392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439910392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000439910392 none O=C(N1CCC[C@@H]([C@@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 15, 15, 15, 15, 15, 18, 25, 25, 25, 25, 25, 15, 1, 1, 1, 6, 6, 11, 11, 6, 11, 11, 11, 15, 15, 15, 15, 15, 15, 25, 25, 25, 25, 25, 25, 15, 15, 6, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 98 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910392 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439910392 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910392/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910392/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910392 Building ZINC000439910394 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910394' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439910394 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910394/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/825 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]([C@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000439910394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439910394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000439910394 none O=C(N1CCC[C@H]([C@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 9, 15, 15, 15, 15, 15, 17, 27, 27, 27, 27, 27, 15, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 15, 15, 15, 15, 15, 15, 27, 27, 27, 27, 27, 27, 15, 15, 6, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 83 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910394/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/826 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/826' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]([C@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000439910394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439910394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000439910394 none O=C(N1CCC[C@H]([C@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 8, 13, 13, 13, 13, 13, 14, 28, 28, 28, 28, 28, 13, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 13, 13, 13, 13, 13, 13, 28, 28, 28, 28, 28, 28, 13, 13, 6, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439910394 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910394/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910394/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910394 Building ZINC000439910394 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910394' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439910394 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910394/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 825) grep: /scratch/xiaobo/83235/xao-8058115.15/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]([C@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000439910394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439910394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000439910394 none O=C(N1CCC[C@H]([C@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 9, 15, 15, 15, 15, 15, 17, 27, 27, 27, 27, 27, 15, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 15, 15, 15, 15, 15, 15, 27, 27, 27, 27, 27, 27, 15, 15, 6, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 83 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910394/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 826) grep: /scratch/xiaobo/83235/xao-8058115.15/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]([C@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000439910394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439910394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000439910394 none O=C(N1CCC[C@H]([C@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 8, 13, 13, 13, 13, 13, 14, 28, 28, 28, 28, 28, 13, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 13, 13, 13, 13, 13, 13, 28, 28, 28, 28, 28, 28, 13, 13, 6, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439910394 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910394/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910394/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910394 Building ZINC000439910395 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910395' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910395 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439910395 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910395/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910395 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/827 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]([C@@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000439910395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439910395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000439910395 none O=C(N1CCC[C@H]([C@@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 9, 13, 13, 13, 13, 13, 15, 26, 26, 26, 26, 26, 13, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 13, 13, 13, 13, 13, 13, 26, 26, 26, 26, 26, 26, 13, 13, 6, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 81 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910395 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910395/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910395 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/828 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/828' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]([C@@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000439910395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439910395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000439910395 none O=C(N1CCC[C@H]([C@@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 8, 13, 13, 13, 13, 13, 14, 27, 27, 27, 27, 27, 13, 1, 1, 1, 6, 6, 9, 9, 6, 9, 9, 9, 13, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 13, 13, 6, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 91 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910395 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439910395 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910395/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910395/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910395 Building ZINC000439910395 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910395' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910395 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439910395 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910395/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910395 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 827) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCC[C@H]([C@@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000439910395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439910395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000439910395 none O=C(N1CCC[C@H]([C@@H]2CCOC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 9, 13, 13, 13, 13, 13, 15, 26, 26, 26, 26, 26, 13, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 13, 13, 13, 13, 13, 13, 26, 26, 26, 26, 26, 26, 13, 13, 6, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 81 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910395 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910395/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910395 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 828) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N1CCC[C@H]([C@@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000439910395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439910395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000439910395 none O=C(N1CCC[C@H]([C@@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 8, 13, 13, 13, 13, 13, 14, 27, 27, 27, 27, 27, 13, 1, 1, 1, 6, 6, 9, 9, 6, 9, 9, 9, 13, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 13, 13, 6, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 91 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910395 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439910395 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910395/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910395/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439910395 Building ZINC000439864571 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864571' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864571 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439864571 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864571/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864571 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/829 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C) `ZINC000439864571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439864571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000439864571 none CO[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C NO_LONG_NAME dock atom types: ['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', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 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, 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: [38, 33, 33, 33, 33, 10, 33, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 33, 33, 33, 38, 38, 38, 33, 33, 6, 6, 6, 6, 6, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864571 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864571/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864571 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/830 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/830' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C) `ZINC000439864571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439864571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000439864571 none CO[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C NO_LONG_NAME dock atom types: ['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', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 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, 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: [38, 32, 32, 32, 32, 10, 32, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 32, 32, 32, 38, 38, 38, 32, 32, 6, 6, 6, 6, 6, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864571 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439864571 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864571/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864571/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864571 Building ZINC000439864571 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864571' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864571 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439864571 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864571/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864571 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 829) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CO[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C) `ZINC000439864571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439864571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000439864571 none CO[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C NO_LONG_NAME dock atom types: ['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', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 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, 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: [38, 33, 33, 33, 33, 10, 33, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 33, 33, 33, 38, 38, 38, 33, 33, 6, 6, 6, 6, 6, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864571 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864571/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864571 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 830) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CO[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C) `ZINC000439864571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439864571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000439864571 none CO[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C NO_LONG_NAME dock atom types: ['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', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 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, 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: [38, 32, 32, 32, 32, 10, 32, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 32, 32, 32, 38, 38, 38, 32, 32, 6, 6, 6, 6, 6, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864571 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439864571 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864571/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864571/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864571 Building ZINC000439864572 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864572' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864572 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439864572 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864572/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864572 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/831 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C) `ZINC000439864572.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439864572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000439864572 none CO[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C NO_LONG_NAME dock atom types: ['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', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 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, 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: [39, 33, 33, 33, 33, 10, 33, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 33, 33, 33, 39, 39, 39, 33, 33, 6, 6, 6, 6, 6, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864572 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864572/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864572 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/832 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/832' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C) `ZINC000439864572.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439864572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864572/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000439864572 none CO[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C NO_LONG_NAME dock atom types: ['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', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 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, 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: [38, 33, 33, 33, 33, 10, 33, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 33, 33, 33, 38, 38, 38, 33, 33, 6, 6, 6, 6, 6, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864572 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439864572 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864572/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864572/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864572 Building ZINC000439864572 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864572' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864572 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439864572 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864572/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864572 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 831) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CO[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C) `ZINC000439864572.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439864572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000439864572 none CO[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C NO_LONG_NAME dock atom types: ['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', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 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, 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: [39, 33, 33, 33, 33, 10, 33, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 33, 33, 33, 39, 39, 39, 33, 33, 6, 6, 6, 6, 6, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864572 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864572/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864572 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 832) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CO[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C) `ZINC000439864572.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439864572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864572/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000439864572 none CO[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C NO_LONG_NAME dock atom types: ['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', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 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, 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: [38, 33, 33, 33, 33, 10, 33, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 33, 33, 33, 38, 38, 38, 33, 33, 6, 6, 6, 6, 6, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864572 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439864572 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864572/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864572/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864572 Building ZINC000439864573 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864573' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864573 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439864573 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864573/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864573 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/833 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C) `ZINC000439864573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439864573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000439864573 none CO[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C NO_LONG_NAME dock atom types: ['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', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 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, 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: [41, 34, 34, 34, 34, 12, 34, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 34, 34, 34, 41, 41, 41, 34, 34, 6, 6, 6, 6, 6, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 123 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864573 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864573/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864573 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/834 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/834' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C) `ZINC000439864573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439864573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000439864573 none CO[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C NO_LONG_NAME dock atom types: ['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', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 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, 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: [39, 33, 33, 33, 33, 12, 33, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 33, 33, 33, 39, 39, 39, 33, 33, 6, 5, 5, 5, 5, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864573 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439864573 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864573/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864573/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864573 Building ZINC000439864573 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864573' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864573 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439864573 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864573/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864573 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 833) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CO[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C) `ZINC000439864573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439864573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000439864573 none CO[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C NO_LONG_NAME dock atom types: ['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', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 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, 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: [41, 34, 34, 34, 34, 12, 34, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 34, 34, 34, 41, 41, 41, 34, 34, 6, 6, 6, 6, 6, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 123 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864573 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864573/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864573 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 834) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CO[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C) `ZINC000439864573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439864573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000439864573 none CO[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C NO_LONG_NAME dock atom types: ['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', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 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, 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: [39, 33, 33, 33, 33, 12, 33, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 33, 33, 33, 39, 39, 39, 33, 33, 6, 5, 5, 5, 5, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864573 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439864573 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864573/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864573/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864573 Building ZINC000439864574 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864574' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864574 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439864574 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864574/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864574 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/835 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C) `ZINC000439864574.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439864574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000439864574 none CO[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C NO_LONG_NAME dock atom types: ['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', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 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, 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: [39, 33, 33, 33, 33, 12, 33, 6, 1, 6, 1, 1, 1, 5, 5, 2, 1, 5, 5, 33, 33, 33, 39, 39, 39, 33, 33, 6, 5, 5, 5, 5, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864574 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864574/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864574 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/836 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/836' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C) `ZINC000439864574.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439864574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000439864574 none CO[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C NO_LONG_NAME dock atom types: ['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', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 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, 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: [42, 36, 36, 36, 36, 12, 36, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 36, 36, 36, 42, 42, 42, 36, 36, 6, 6, 6, 6, 6, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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/83235/xao-8058115.15/working/building/ZINC000439864574 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439864574 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864574/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864574/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864574 Building ZINC000439864574 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864574' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864574 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439864574 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864574/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864574 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 835) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CO[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C) `ZINC000439864574.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439864574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000439864574 none CO[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C NO_LONG_NAME dock atom types: ['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', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 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, 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: [39, 33, 33, 33, 33, 12, 33, 6, 1, 6, 1, 1, 1, 5, 5, 2, 1, 5, 5, 33, 33, 33, 39, 39, 39, 33, 33, 6, 5, 5, 5, 5, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864574 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864574/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864574 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 836) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CO[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C) `ZINC000439864574.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439864574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000439864574 none CO[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1(C)C NO_LONG_NAME dock atom types: ['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', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 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, 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: [42, 36, 36, 36, 36, 12, 36, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 36, 36, 36, 42, 42, 42, 36, 36, 6, 6, 6, 6, 6, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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/83235/xao-8058115.15/working/building/ZINC000439864574 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000439864574 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864574/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864574/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000439864574 Building ZINC000761921011 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921011' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921011 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000761921011 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921011/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921011 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/837 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CCO)c1cccs1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000761921011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000761921011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000761921011 none O=C(N[C@@H](CCO)c1cccs1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 6, 6, 15, 15, 6, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 15, 15, 15, 15, 45, 18, 18, 18, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 132 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921011 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921011/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921011 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/838 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/838' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CCO)c1cccs1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000761921011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000761921011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000761921011 none O=C(N[C@@H](CCO)c1cccs1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 6, 6, 15, 15, 6, 16, 16, 16, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 15, 15, 15, 15, 45, 16, 16, 16, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 130 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921011 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000761921011 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921011/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921011/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921011 Building ZINC000761921011 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921011' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921011 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000761921011 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921011/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921011 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 837) grep: /scratch/xiaobo/83235/xao-8058115.15/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](CCO)c1cccs1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000761921011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000761921011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000761921011 none O=C(N[C@@H](CCO)c1cccs1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 6, 6, 15, 15, 6, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 15, 15, 15, 15, 45, 18, 18, 18, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 132 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921011 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921011/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921011 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 838) grep: /scratch/xiaobo/83235/xao-8058115.15/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](CCO)c1cccs1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000761921011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000761921011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000761921011 none O=C(N[C@@H](CCO)c1cccs1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 6, 6, 15, 15, 6, 16, 16, 16, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 15, 15, 15, 15, 45, 16, 16, 16, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 130 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921011 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000761921011 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921011/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921011/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921011 Building ZINC000761921012 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921012' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921012 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000761921012 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921012/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921012 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/839 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](CCO)c1cccs1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000761921012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000761921012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000761921012 none O=C(N[C@H](CCO)c1cccs1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 6, 6, 15, 15, 6, 16, 16, 16, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 15, 15, 15, 15, 45, 16, 16, 16, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 130 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921012 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921012/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921012 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/840 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/840' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](CCO)c1cccs1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000761921012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000761921012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000761921012 none O=C(N[C@H](CCO)c1cccs1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 6, 6, 15, 15, 6, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 15, 15, 15, 15, 45, 18, 18, 18, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 132 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921012 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000761921012 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921012/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921012/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921012 Building ZINC000761921012 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921012' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921012 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000761921012 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921012/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921012 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 839) grep: /scratch/xiaobo/83235/xao-8058115.15/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](CCO)c1cccs1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000761921012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000761921012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000761921012 none O=C(N[C@H](CCO)c1cccs1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 6, 6, 15, 15, 6, 16, 16, 16, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 15, 15, 15, 15, 45, 16, 16, 16, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 130 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921012 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921012/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921012 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 840) grep: /scratch/xiaobo/83235/xao-8058115.15/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](CCO)c1cccs1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000761921012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000761921012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000761921012 none O=C(N[C@H](CCO)c1cccs1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 6, 6, 15, 15, 6, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 15, 15, 15, 15, 45, 18, 18, 18, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 132 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921012 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000761921012 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921012/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921012/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000761921012 Building ZINC000441278358 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441278358' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441278358 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000441278358 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441278358/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441278358 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/841 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(C)(C)C) `ZINC000441278358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000441278358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441278358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC000441278358 none CCOC(=O)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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, 3, 7, 5, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 10, 19, 10, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 10, 10, 10, 10, 28, 28, 28, 28, 28, 10, 10, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 99 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441278358 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441278358/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441278358 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/842 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/842' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(C)(C)C) `ZINC000441278358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000441278358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441278358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC000441278358 none CCOC(=O)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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, 3, 7, 5, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 19, 18, 10, 18, 10, 5, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 10, 10, 10, 10, 30, 30, 30, 30, 30, 10, 10, 12, 12, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 111 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441278358 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000441278358 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441278358/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441278358/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441278358 Building ZINC000441278358 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441278358' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441278358 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000441278358 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441278358/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441278358 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 841) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCOC(=O)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(C)(C)C) `ZINC000441278358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000441278358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441278358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC000441278358 none CCOC(=O)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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, 3, 7, 5, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 10, 19, 10, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 10, 10, 10, 10, 28, 28, 28, 28, 28, 10, 10, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 99 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441278358 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441278358/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441278358 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 842) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCOC(=O)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(C)(C)C) `ZINC000441278358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000441278358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441278358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC000441278358 none CCOC(=O)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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, 3, 7, 5, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 19, 18, 10, 18, 10, 5, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 10, 10, 10, 10, 30, 30, 30, 30, 30, 10, 10, 12, 12, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 111 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441278358 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000441278358 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441278358/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441278358/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441278358 Building ZINC000337336531 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337336531' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337336531 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337336531 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337336531/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337336531 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/843 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCOc2ccccc2Cl)cn1) `ZINC000337336531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337336531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337336531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337336531 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCOc2ccccc2Cl)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 11, 25, 37, 37, 25, 37, 37, 37, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 7, 7, 11, 11, 37, 37, 26, 37, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337336531 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337336531/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337336531 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/844 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/844' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCOc2ccccc2Cl)cn1) `ZINC000337336531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337336531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337336531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337336531 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCOc2ccccc2Cl)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 8, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 11, 25, 37, 37, 25, 37, 37, 37, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 7, 7, 11, 11, 37, 37, 29, 37, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337336531 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337336531 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337336531/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337336531/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337336531 Building ZINC000337336531 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337336531' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337336531 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337336531 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337336531/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337336531 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 843) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCOc2ccccc2Cl)cn1) `ZINC000337336531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337336531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337336531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337336531 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCOc2ccccc2Cl)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 11, 25, 37, 37, 25, 37, 37, 37, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 7, 7, 11, 11, 37, 37, 26, 37, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337336531 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337336531/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337336531 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 844) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCOc2ccccc2Cl)cn1) `ZINC000337336531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337336531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337336531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337336531 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCOc2ccccc2Cl)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 8, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 11, 25, 37, 37, 25, 37, 37, 37, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 7, 7, 11, 11, 37, 37, 29, 37, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337336531 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000337336531 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337336531/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337336531/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000337336531 Building ZINC000441465162 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465162' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465162 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000441465162 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465162/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465162 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/845 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)C1) `ZINC000441465162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000441465162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000441465162 none CO[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 31, 31, 20, 2, 20, 1, 1, 1, 4, 4, 1, 1, 4, 4, 31, 31, 31, 31, 43, 43, 43, 31, 31, 31, 31, 4, 4, 4, 4, 31, 31, 31, 31, 31] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 95 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465162 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465162/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465162 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/846 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/846' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)C1) `ZINC000441465162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000441465162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000441465162 none CO[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 34, 21, 2, 21, 1, 1, 1, 4, 4, 1, 1, 4, 4, 34, 34, 34, 34, 45, 45, 45, 34, 34, 34, 34, 4, 4, 4, 4, 34, 34, 34, 34, 34] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 93 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465162 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000441465162 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465162/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465162/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465162 Building ZINC000441465162 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465162' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465162 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000441465162 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465162/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465162 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 845) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CO[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)C1) `ZINC000441465162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000441465162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000441465162 none CO[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 31, 31, 20, 2, 20, 1, 1, 1, 4, 4, 1, 1, 4, 4, 31, 31, 31, 31, 43, 43, 43, 31, 31, 31, 31, 4, 4, 4, 4, 31, 31, 31, 31, 31] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 95 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465162 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465162/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465162 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 846) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CO[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)C1) `ZINC000441465162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000441465162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000441465162 none CO[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 34, 21, 2, 21, 1, 1, 1, 4, 4, 1, 1, 4, 4, 34, 34, 34, 34, 45, 45, 45, 34, 34, 34, 34, 4, 4, 4, 4, 34, 34, 34, 34, 34] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 93 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465162 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000441465162 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465162/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465162/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465162 Building ZINC000441465163 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465163' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465163 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000441465163 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465163/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465163 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/847 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)C1) `ZINC000441465163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000441465163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000441465163 none CO[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [42, 30, 30, 30, 30, 30, 20, 2, 20, 1, 1, 1, 4, 4, 1, 4, 4, 4, 30, 30, 30, 30, 42, 42, 42, 30, 30, 30, 30, 4, 4, 4, 4, 30, 30, 30, 30, 30] 46 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 96 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465163 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465163/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465163 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/848 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/848' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)C1) `ZINC000441465163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000441465163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000441465163 none CO[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 31, 31, 19, 2, 19, 1, 1, 1, 4, 4, 1, 4, 4, 4, 31, 31, 31, 31, 43, 43, 43, 31, 31, 31, 31, 4, 4, 4, 4, 31, 31, 31, 31, 31] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 96 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465163 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000441465163 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465163/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465163/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465163 Building ZINC000441465163 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465163' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465163 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000441465163 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465163/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465163 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 847) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CO[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)C1) `ZINC000441465163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000441465163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000441465163 none CO[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [42, 30, 30, 30, 30, 30, 20, 2, 20, 1, 1, 1, 4, 4, 1, 4, 4, 4, 30, 30, 30, 30, 42, 42, 42, 30, 30, 30, 30, 4, 4, 4, 4, 30, 30, 30, 30, 30] 46 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 96 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465163 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465163/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465163 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 848) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CO[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)C1) `ZINC000441465163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000441465163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000441465163 none CO[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 31, 31, 19, 2, 19, 1, 1, 1, 4, 4, 1, 4, 4, 4, 31, 31, 31, 31, 43, 43, 43, 31, 31, 31, 31, 4, 4, 4, 4, 31, 31, 31, 31, 31] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 96 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465163 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000441465163 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465163/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465163/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465163 Building ZINC000441465164 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465164' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465164 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000441465164 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465164/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465164 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/849 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)C1) `ZINC000441465164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000441465164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000441465164 none CO[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 20, 20, 20, 20, 20, 11, 1, 11, 1, 1, 1, 6, 6, 1, 1, 6, 6, 20, 20, 20, 20, 32, 32, 32, 20, 20, 20, 20, 6, 6, 6, 6, 20, 20, 20, 20, 20] 39 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: 73 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465164 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465164/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465164 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/850 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/850' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)C1) `ZINC000441465164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000441465164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000441465164 none CO[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [28, 17, 17, 17, 17, 17, 12, 1, 12, 1, 1, 1, 5, 5, 1, 1, 5, 5, 17, 17, 17, 17, 28, 28, 28, 17, 17, 17, 17, 5, 5, 5, 5, 17, 17, 17, 17, 17] 31 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: 65 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465164 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000441465164 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465164/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465164/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465164 Building ZINC000441465164 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465164' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465164 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000441465164 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465164/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465164 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 849) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CO[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)C1) `ZINC000441465164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000441465164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000441465164 none CO[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 20, 20, 20, 20, 20, 11, 1, 11, 1, 1, 1, 6, 6, 1, 1, 6, 6, 20, 20, 20, 20, 32, 32, 32, 20, 20, 20, 20, 6, 6, 6, 6, 20, 20, 20, 20, 20] 39 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: 73 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465164 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465164/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465164 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 850) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CO[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)C1) `ZINC000441465164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000441465164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000441465164 none CO[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [28, 17, 17, 17, 17, 17, 12, 1, 12, 1, 1, 1, 5, 5, 1, 1, 5, 5, 17, 17, 17, 17, 28, 28, 28, 17, 17, 17, 17, 5, 5, 5, 5, 17, 17, 17, 17, 17] 31 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: 65 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465164 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000441465164 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465164/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465164/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465164 Building ZINC000441465165 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465165' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465165 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000441465165 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465165/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465165 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/851 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)C1) `ZINC000441465165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000441465165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000441465165 none CO[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 23, 23, 23, 23, 23, 13, 2, 13, 1, 1, 1, 4, 4, 1, 1, 4, 4, 23, 23, 23, 23, 32, 32, 32, 23, 23, 23, 23, 4, 4, 4, 4, 23, 23, 23, 23, 23] 38 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 71 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465165 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465165/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465165 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/852 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/852' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)C1) `ZINC000441465165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000441465165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000441465165 none CO[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [28, 22, 22, 22, 22, 22, 14, 2, 14, 1, 1, 1, 4, 4, 1, 1, 4, 4, 22, 22, 22, 22, 28, 28, 28, 22, 22, 22, 22, 4, 4, 4, 4, 22, 22, 22, 22, 22] 33 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 65 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465165 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000441465165 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465165/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465165/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465165 Building ZINC000441465165 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465165' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465165 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000441465165 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465165/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465165 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 851) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/851: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)C1) `ZINC000441465165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000441465165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000441465165 none CO[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 23, 23, 23, 23, 23, 13, 2, 13, 1, 1, 1, 4, 4, 1, 1, 4, 4, 23, 23, 23, 23, 32, 32, 32, 23, 23, 23, 23, 4, 4, 4, 4, 23, 23, 23, 23, 23] 38 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 71 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465165 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465165/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465165 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 852) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/852: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)C1) `ZINC000441465165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000441465165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000441465165 none CO[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [28, 22, 22, 22, 22, 22, 14, 2, 14, 1, 1, 1, 4, 4, 1, 1, 4, 4, 22, 22, 22, 22, 28, 28, 28, 22, 22, 22, 22, 4, 4, 4, 4, 22, 22, 22, 22, 22] 33 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 65 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465165 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000441465165 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465165/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465165/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000441465165 Building ZINC000540985020 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000540985020' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000540985020 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540985020 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000540985020/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000540985020 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/853 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000540985020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540985020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000540985020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000540985020 none COC(=O)CN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 15, 1, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 31, 7, 3, 7, 26, 29, 29, 27, 29, 29, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 31, 31, 31, 14, 14, 26, 26, 29, 29, 29, 29, 29, 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]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000540985020 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000540985020/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000540985020 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/854 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/854' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000540985020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540985020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000540985020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000540985020 none COC(=O)CN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 15, 1, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 32, 6, 2, 6, 24, 27, 27, 24, 27, 27, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 13, 13, 24, 24, 27, 27, 24, 27, 27, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000540985020 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000540985020 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000540985020/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000540985020/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000540985020 Building ZINC000540985020 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000540985020' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000540985020 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540985020 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000540985020/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000540985020 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 853) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC(=O)CN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000540985020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540985020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000540985020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000540985020 none COC(=O)CN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 15, 1, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 31, 7, 3, 7, 26, 29, 29, 27, 29, 29, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 31, 31, 31, 14, 14, 26, 26, 29, 29, 29, 29, 29, 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]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000540985020 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000540985020/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000540985020 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 854) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COC(=O)CN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000540985020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540985020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000540985020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000540985020 none COC(=O)CN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 15, 1, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 32, 6, 2, 6, 24, 27, 27, 24, 27, 27, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 13, 13, 24, 24, 27, 27, 24, 27, 27, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000540985020 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000540985020 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000540985020/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000540985020/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000540985020 Building ZINC000176068142 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000176068142' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000176068142 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000176068142 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000176068142/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000176068142 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/855 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C)c(Br)cn2)cc1) `ZINC000176068142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000176068142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000176068142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000176068142 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C)c(Br)cn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 1, 17, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 1, 11, 11, 1, 1, 1, 1, 10, 10, 10, 19, 19, 19, 19, 19, 19, 19, 11, 11, 11, 11, 11, 11, 11, 10, 19, 19, 19, 19, 19, 11, 11] 37 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000176068142 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000176068142/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000176068142 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/856 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/856' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C)c(Br)cn2)cc1) `ZINC000176068142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000176068142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000176068142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000176068142 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C)c(Br)cn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 1, 17, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 1, 11, 11, 1, 1, 1, 1, 10, 10, 10, 19, 19, 19, 19, 19, 19, 19, 11, 11, 11, 11, 11, 11, 11, 10, 19, 19, 19, 19, 19, 11, 11] 37 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000176068142 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000176068142 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000176068142/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000176068142/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000176068142 Building ZINC000176068142 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000176068142' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000176068142 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000176068142 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000176068142/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000176068142 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 855) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/855: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C)c(Br)cn2)cc1) `ZINC000176068142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000176068142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000176068142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000176068142 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C)c(Br)cn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 1, 17, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 1, 11, 11, 1, 1, 1, 1, 10, 10, 10, 19, 19, 19, 19, 19, 19, 19, 11, 11, 11, 11, 11, 11, 11, 10, 19, 19, 19, 19, 19, 11, 11] 37 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000176068142 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000176068142/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000176068142 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 856) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/856: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C)c(Br)cn2)cc1) `ZINC000176068142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000176068142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000176068142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000176068142 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C)c(Br)cn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 1, 17, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 1, 11, 11, 1, 1, 1, 1, 10, 10, 10, 19, 19, 19, 19, 19, 19, 19, 11, 11, 11, 11, 11, 11, 11, 10, 19, 19, 19, 19, 19, 11, 11] 37 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000176068142 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000176068142 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000176068142/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000176068142/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000176068142 Building ZINC000442824435 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824435' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824435 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000442824435 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824435/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824435 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/857 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/857' -> `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)c1ncc[nH]1) `ZINC000442824435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000442824435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000442824435 none CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)c1ncc[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', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 17, 1, 1, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 13, 6, 13, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 5, 13, 34, 34, 34, 34, 34, 30, 30, 30, 30, 30, 6, 5, 5, 5, 5, 34, 34] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824435 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824435/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824435 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/858 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/858' -> `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)c1ncc[nH]1) `ZINC000442824435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000442824435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000442824435 none CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)c1ncc[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', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 17, 1, 1, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 13, 6, 13, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 13, 38, 38, 38, 38, 38, 31, 31, 31, 31, 31, 6, 5, 5, 5, 5, 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]) total number of confs: 176 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824435 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000442824435 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824435/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824435/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824435 Building ZINC000442824435 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824435' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824435 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000442824435 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824435/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824435 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 857) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/857: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)c1ncc[nH]1) `ZINC000442824435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000442824435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000442824435 none CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)c1ncc[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', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 17, 1, 1, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 13, 6, 13, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 5, 13, 34, 34, 34, 34, 34, 30, 30, 30, 30, 30, 6, 5, 5, 5, 5, 34, 34] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824435 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824435/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824435 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 858) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/858: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)c1ncc[nH]1) `ZINC000442824435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000442824435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000442824435 none CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)c1ncc[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', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 17, 1, 1, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 13, 6, 13, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 13, 38, 38, 38, 38, 38, 31, 31, 31, 31, 31, 6, 5, 5, 5, 5, 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]) total number of confs: 176 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824435 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000442824435 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824435/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824435/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824435 Building ZINC000442824437 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824437' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824437 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000442824437 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824437/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824437 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/859 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/859' -> `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)c1ncc[nH]1) `ZINC000442824437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000442824437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000442824437 none CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)c1ncc[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', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 17, 1, 1, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 13, 6, 13, 6, 1, 6, 1, 1, 1, 5, 5, 2, 5, 5, 5, 13, 31, 31, 31, 31, 31, 30, 30, 30, 30, 30, 6, 5, 5, 5, 5, 31, 31] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824437 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824437/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824437 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/860 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/860' -> `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)c1ncc[nH]1) `ZINC000442824437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000442824437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000442824437 none CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)c1ncc[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', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 17, 1, 1, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 13, 6, 13, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 5, 13, 29, 29, 29, 29, 29, 30, 30, 30, 30, 30, 6, 5, 5, 5, 5, 29, 29] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824437 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000442824437 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824437/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824437/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824437 Building ZINC000442824437 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824437' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824437 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000442824437 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824437/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824437 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 859) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)c1ncc[nH]1) `ZINC000442824437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000442824437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000442824437 none CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)c1ncc[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', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 17, 1, 1, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 13, 6, 13, 6, 1, 6, 1, 1, 1, 5, 5, 2, 5, 5, 5, 13, 31, 31, 31, 31, 31, 30, 30, 30, 30, 30, 6, 5, 5, 5, 5, 31, 31] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824437 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824437/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824437 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 860) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)c1ncc[nH]1) `ZINC000442824437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000442824437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000442824437 none CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)c1ncc[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', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 17, 1, 1, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 13, 6, 13, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 5, 13, 29, 29, 29, 29, 29, 30, 30, 30, 30, 30, 6, 5, 5, 5, 5, 29, 29] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824437 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000442824437 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824437/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824437/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000442824437 Building ZINC000164900925 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000164900925' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000164900925 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000164900925 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000164900925/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000164900925 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/861 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](C(=O)OC(C)(C)C)C2)cc1) `ZINC000164900925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000164900925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000164900925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000164900925 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](C(=O)OC(C)(C)C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 9, 9, 33, 33, 36, 36, 36, 36, 9, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 36, 36, 36, 36, 36, 36, 36, 36, 36, 9, 9, 3, 3] 36 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 99 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000164900925 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000164900925/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000164900925 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/862 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/862' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](C(=O)OC(C)(C)C)C2)cc1) `ZINC000164900925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000164900925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000164900925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000164900925 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](C(=O)OC(C)(C)C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 2, 4, 5, 7, 7, 7, 7, 7, 7, 36, 36, 50, 50, 50, 50, 7, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 3, 3] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000164900925 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000164900925 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000164900925/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000164900925/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000164900925 Building ZINC000164900925 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000164900925' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000164900925 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000164900925 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000164900925/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000164900925 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 861) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](C(=O)OC(C)(C)C)C2)cc1) `ZINC000164900925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000164900925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000164900925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000164900925 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](C(=O)OC(C)(C)C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 9, 9, 33, 33, 36, 36, 36, 36, 9, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 36, 36, 36, 36, 36, 36, 36, 36, 36, 9, 9, 3, 3] 36 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 99 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000164900925 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000164900925/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000164900925 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 862) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](C(=O)OC(C)(C)C)C2)cc1) `ZINC000164900925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000164900925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000164900925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000164900925 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](C(=O)OC(C)(C)C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 2, 4, 5, 7, 7, 7, 7, 7, 7, 36, 36, 50, 50, 50, 50, 7, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 3, 3] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000164900925 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000164900925 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000164900925/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000164900925/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000164900925 Building ZINC000541582064 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582064' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582064 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541582064 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582064/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582064 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/863 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccnc1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1) `ZINC000541582064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541582064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000541582064 none Cn1ccnc1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 6, 11, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 11, 27, 27, 11, 27, 27, 39, 39, 39, 39, 39, 6, 4, 4, 4, 4, 27, 27, 12, 27, 27] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 154 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582064 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582064/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582064 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/864 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/864' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccnc1[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1) `ZINC000541582064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541582064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000541582064 none Cn1ccnc1[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 6, 10, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 10, 26, 26, 10, 26, 26, 39, 39, 39, 39, 39, 6, 4, 4, 4, 4, 26, 26, 12, 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]) total number of confs: 151 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582064 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000541582064 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582064/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582064/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582064 Building ZINC000541582064 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582064' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582064 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541582064 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582064/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582064 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 863) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cn1ccnc1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1) `ZINC000541582064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541582064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000541582064 none Cn1ccnc1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 6, 11, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 11, 27, 27, 11, 27, 27, 39, 39, 39, 39, 39, 6, 4, 4, 4, 4, 27, 27, 12, 27, 27] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 154 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582064 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582064/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582064 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 864) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cn1ccnc1[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1) `ZINC000541582064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541582064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000541582064 none Cn1ccnc1[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 6, 10, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 10, 26, 26, 10, 26, 26, 39, 39, 39, 39, 39, 6, 4, 4, 4, 4, 26, 26, 12, 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]) total number of confs: 151 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582064 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000541582064 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582064/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582064/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582064 Building ZINC000541582067 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582067' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582067 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541582067 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582067/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582067 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/865 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccnc1[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1) `ZINC000541582067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541582067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000541582067 none Cn1ccnc1[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 10, 6, 10, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 10, 26, 26, 10, 26, 26, 38, 38, 38, 38, 38, 6, 4, 4, 4, 4, 26, 26, 10, 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]) total number of confs: 146 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582067 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582067/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582067 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/866 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/866' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccnc1[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1) `ZINC000541582067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541582067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000541582067 none Cn1ccnc1[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 6, 11, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 11, 27, 27, 11, 27, 27, 39, 39, 39, 39, 39, 6, 4, 4, 4, 4, 27, 27, 11, 27, 27] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 152 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582067 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000541582067 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582067/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582067/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582067 Building ZINC000541582067 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582067' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582067 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541582067 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582067/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582067 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 865) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/865: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccnc1[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1) `ZINC000541582067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541582067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000541582067 none Cn1ccnc1[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 10, 6, 10, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 10, 26, 26, 10, 26, 26, 38, 38, 38, 38, 38, 6, 4, 4, 4, 4, 26, 26, 10, 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]) total number of confs: 146 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582067 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582067/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582067 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 866) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/866: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccnc1[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1) `ZINC000541582067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541582067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000541582067 none Cn1ccnc1[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 6, 11, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 11, 27, 27, 11, 27, 27, 39, 39, 39, 39, 39, 6, 4, 4, 4, 4, 27, 27, 11, 27, 27] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 152 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582067 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000541582067 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582067/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582067/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541582067 Building ZINC000541621921 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541621921' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541621921 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541621921 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541621921/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541621921 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/867 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCCC1) `ZINC000541621921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541621921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541621921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000541621921 none CC(C)(C)OC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 50, 38, 13, 38, 5, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541621921 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541621921/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541621921 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/868 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/868' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCCC1) `ZINC000541621921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541621921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541621921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000541621921 none CC(C)(C)OC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 50, 50, 38, 14, 38, 5, 5, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541621921 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000541621921 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541621921/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541621921/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541621921 Building ZINC000541621921 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541621921' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541621921 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541621921 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541621921/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541621921 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 867) grep: /scratch/xiaobo/83235/xao-8058115.15/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)(C)OC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCCC1) `ZINC000541621921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541621921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541621921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000541621921 none CC(C)(C)OC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 50, 38, 13, 38, 5, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541621921 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541621921/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541621921 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 868) grep: /scratch/xiaobo/83235/xao-8058115.15/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)(C)OC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCCC1) `ZINC000541621921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541621921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541621921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000541621921 none CC(C)(C)OC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 50, 50, 38, 14, 38, 5, 5, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541621921 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000541621921 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541621921/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541621921/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541621921 Building ZINC000762320398 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762320398' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762320398 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000762320398 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762320398/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762320398 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/869 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(c3cn[nH]c3)c2)cn1) `ZINC000762320398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000762320398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762320398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000762320398 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(c3cn[nH]c3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 8, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 12, 22, 22, 22, 22, 22, 12, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 12, 12, 12, 22, 22, 12, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762320398 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762320398/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762320398 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/870 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/870' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(c3cn[nH]c3)c2)cn1) `ZINC000762320398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000762320398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762320398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000762320398 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(c3cn[nH]c3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 8, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 12, 22, 22, 22, 22, 22, 12, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 12, 12, 12, 22, 22, 12, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762320398 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000762320398 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762320398/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762320398/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762320398 Building ZINC000762320398 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762320398' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762320398 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000762320398 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762320398/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762320398 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 869) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/869: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(c3cn[nH]c3)c2)cn1) `ZINC000762320398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000762320398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762320398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000762320398 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(c3cn[nH]c3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 8, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 12, 22, 22, 22, 22, 22, 12, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 12, 12, 12, 22, 22, 12, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762320398 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762320398/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762320398 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 870) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/870: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(c3cn[nH]c3)c2)cn1) `ZINC000762320398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000762320398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762320398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000762320398 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(c3cn[nH]c3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 8, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 12, 22, 22, 22, 22, 22, 12, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 12, 12, 12, 22, 22, 12, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762320398 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000762320398 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762320398/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762320398/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762320398 Building ZINC000541680333 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541680333' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541680333 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541680333 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541680333/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541680333 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/871 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C)C)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000541680333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541680333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541680333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000541680333 none COc1ccc(CN(C)C)cc1NC(=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.3', 'N.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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 10, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 12, 12, 12, 8, 12, 12, 42, 44, 44, 12, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 12, 12, 42, 42, 44, 44, 44, 44, 44, 44, 12, 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, 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/83235/xao-8058115.15/working/building/ZINC000541680333 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541680333/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541680333 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/872 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/872' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C)C)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000541680333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541680333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541680333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000541680333 none COc1ccc(CN(C)C)cc1NC(=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.3', 'N.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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 10, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 12, 12, 12, 12, 12, 12, 40, 44, 44, 12, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 12, 12, 40, 40, 44, 44, 44, 44, 44, 44, 12, 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, 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/83235/xao-8058115.15/working/building/ZINC000541680333 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000541680333 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541680333/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541680333/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541680333 Building ZINC000541680333 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541680333' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541680333 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541680333 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541680333/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541680333 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 871) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc(CN(C)C)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000541680333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541680333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541680333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000541680333 none COc1ccc(CN(C)C)cc1NC(=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.3', 'N.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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 10, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 12, 12, 12, 8, 12, 12, 42, 44, 44, 12, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 12, 12, 42, 42, 44, 44, 44, 44, 44, 44, 12, 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, 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/83235/xao-8058115.15/working/building/ZINC000541680333 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541680333/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541680333 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 872) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc(CN(C)C)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000541680333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541680333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541680333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000541680333 none COc1ccc(CN(C)C)cc1NC(=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.3', 'N.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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 10, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 12, 12, 12, 12, 12, 12, 40, 44, 44, 12, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 12, 12, 40, 40, 44, 44, 44, 44, 44, 44, 12, 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, 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/83235/xao-8058115.15/working/building/ZINC000541680333 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000541680333 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541680333/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541680333/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541680333 Building ZINC000541667467 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667467' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667467 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541667467 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667467/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667467 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/873 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/873' -> `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)c2ccccc2N(C)C1=O) `ZINC000541667467.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541667467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000541667467 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2ccccc2N(C)C1=O 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 7, 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, 6, 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: [37, 37, 37, 37, 28, 1, 28, 1, 1, 1, 3, 3, 1, 2, 3, 3, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 3, 3, 3, 3, 37, 37, 37, 37, 37, 37, 37] 39 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667467 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667467/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667467 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/874 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/874' -> `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)c2ccccc2N(C)C1=O) `ZINC000541667467.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541667467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000541667467 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2ccccc2N(C)C1=O 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 33, 1, 33, 1, 1, 1, 4, 4, 1, 1, 4, 4, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 46, 46, 46, 46, 46, 46, 46] 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: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667467 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000541667467 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667467/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667467/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667467 Building ZINC000541667467 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667467' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667467 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541667467 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667467/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667467 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 873) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2ccccc2N(C)C1=O) `ZINC000541667467.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541667467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000541667467 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2ccccc2N(C)C1=O 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 7, 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, 6, 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: [37, 37, 37, 37, 28, 1, 28, 1, 1, 1, 3, 3, 1, 2, 3, 3, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 3, 3, 3, 3, 37, 37, 37, 37, 37, 37, 37] 39 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667467 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667467/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667467 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 874) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2ccccc2N(C)C1=O) `ZINC000541667467.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541667467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000541667467 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2ccccc2N(C)C1=O 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 33, 1, 33, 1, 1, 1, 4, 4, 1, 1, 4, 4, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 46, 46, 46, 46, 46, 46, 46] 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: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667467 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000541667467 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667467/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667467/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667467 Building ZINC000541667468 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667468' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667468 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541667468 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667468/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667468 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/875 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/875' -> `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)c2ccccc2N(C)C1=O) `ZINC000541667468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541667468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000541667468 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2ccccc2N(C)C1=O 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 7, 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, 6, 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, 30, 1, 30, 1, 1, 1, 4, 4, 2, 2, 4, 4, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 45, 45, 45, 45, 45, 45, 45] 49 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]) total number of confs: 97 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667468 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667468/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667468 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/876 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/876' -> `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)c2ccccc2N(C)C1=O) `ZINC000541667468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541667468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000541667468 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2ccccc2N(C)C1=O 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 7, 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, 6, 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: [34, 34, 34, 34, 26, 1, 26, 1, 1, 1, 3, 3, 2, 2, 3, 3, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 3, 3, 3, 3, 34, 34, 34, 34, 34, 34, 34] 36 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667468 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000541667468 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667468/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667468/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667468 Building ZINC000541667468 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667468' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667468 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541667468 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667468/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667468 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 875) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2ccccc2N(C)C1=O) `ZINC000541667468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541667468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000541667468 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2ccccc2N(C)C1=O 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 7, 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, 6, 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, 30, 1, 30, 1, 1, 1, 4, 4, 2, 2, 4, 4, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 45, 45, 45, 45, 45, 45, 45] 49 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]) total number of confs: 97 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667468 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667468/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667468 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 876) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2ccccc2N(C)C1=O) `ZINC000541667468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541667468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000541667468 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2ccccc2N(C)C1=O 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 7, 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, 6, 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: [34, 34, 34, 34, 26, 1, 26, 1, 1, 1, 3, 3, 2, 2, 3, 3, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 3, 3, 3, 3, 34, 34, 34, 34, 34, 34, 34] 36 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667468 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000541667468 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667468/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667468/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541667468 Building ZINC000541721930 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541721930' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541721930 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541721930 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541721930/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541721930 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/877 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(O)c1) `ZINC000541721930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541721930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541721930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000541721930 none CCOC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(O)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.3', '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, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 42, 11, 42, 9, 11, 11, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 11, 11, 50, 50, 50, 50, 50, 11, 11, 4, 3, 3, 3, 3, 22, 11] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541721930 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541721930/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541721930 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/878 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/878' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(O)c1) `ZINC000541721930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541721930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541721930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000541721930 none CCOC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(O)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.3', '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, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 41, 11, 41, 9, 11, 11, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 11, 11, 50, 50, 50, 50, 50, 11, 11, 4, 3, 3, 3, 3, 22, 11] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541721930 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000541721930 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541721930/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541721930/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541721930 Building ZINC000541721930 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541721930' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541721930 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541721930 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541721930/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541721930 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 877) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCOC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(O)c1) `ZINC000541721930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541721930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541721930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000541721930 none CCOC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(O)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.3', '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, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 42, 11, 42, 9, 11, 11, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 11, 11, 50, 50, 50, 50, 50, 11, 11, 4, 3, 3, 3, 3, 22, 11] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541721930 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541721930/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541721930 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 878) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCOC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(O)c1) `ZINC000541721930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541721930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541721930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000541721930 none CCOC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(O)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.3', '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, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 41, 11, 41, 9, 11, 11, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 11, 11, 50, 50, 50, 50, 50, 11, 11, 4, 3, 3, 3, 3, 22, 11] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541721930 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000541721930 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541721930/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541721930/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541721930 Building ZINC000541724308 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724308' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724308 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541724308 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724308/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724308 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/879 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/879' -> `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)c1ccco1) `ZINC000541724308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541724308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000541724308 none O=C(C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccco1 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', 'O.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, 12, 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, 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: [43, 21, 9, 9, 9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 43, 50, 50, 50, 50, 21, 21, 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: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724308 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724308/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724308 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/880 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/880' -> `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)c1ccco1) `ZINC000541724308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541724308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000541724308 none O=C(C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccco1 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', 'O.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, 12, 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, 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: [41, 14, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 41, 50, 50, 50, 50, 14, 14, 5, 5, 5, 5, 5, 5, 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: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724308 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000541724308 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724308/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724308/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724308 Building ZINC000541724308 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724308' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724308 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541724308 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724308/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724308 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 879) grep: /scratch/xiaobo/83235/xao-8058115.15/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(C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccco1) `ZINC000541724308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541724308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000541724308 none O=C(C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccco1 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', 'O.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, 12, 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, 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: [43, 21, 9, 9, 9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 43, 50, 50, 50, 50, 21, 21, 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: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724308 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724308/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724308 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 880) grep: /scratch/xiaobo/83235/xao-8058115.15/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(C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccco1) `ZINC000541724308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541724308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000541724308 none O=C(C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccco1 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', 'O.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, 12, 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, 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: [41, 14, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 41, 50, 50, 50, 50, 14, 14, 5, 5, 5, 5, 5, 5, 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: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724308 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000541724308 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724308/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724308/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724308 Building ZINC000541724309 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724309' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724309 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541724309 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724309/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724309 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/881 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/881' -> `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)c1ccco1) `ZINC000541724309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541724309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000541724309 none O=C(C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccco1 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', 'O.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, 12, 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, 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: [41, 14, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 41, 50, 50, 50, 50, 14, 14, 5, 5, 5, 5, 5, 5, 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: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724309 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724309/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724309 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/882 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/882' -> `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)c1ccco1) `ZINC000541724309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541724309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000541724309 none O=C(C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccco1 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', 'O.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, 12, 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, 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: [43, 21, 9, 9, 9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 43, 50, 50, 50, 50, 21, 21, 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: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724309 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000541724309 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724309/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724309/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724309 Building ZINC000541724309 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724309' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724309 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541724309 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724309/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724309 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 881) grep: /scratch/xiaobo/83235/xao-8058115.15/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(C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccco1) `ZINC000541724309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541724309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000541724309 none O=C(C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccco1 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', 'O.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, 12, 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, 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: [41, 14, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 41, 50, 50, 50, 50, 14, 14, 5, 5, 5, 5, 5, 5, 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: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724309 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724309/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724309 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 882) grep: /scratch/xiaobo/83235/xao-8058115.15/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(C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccco1) `ZINC000541724309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541724309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000541724309 none O=C(C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccco1 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', 'O.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, 12, 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, 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: [43, 21, 9, 9, 9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 43, 50, 50, 50, 50, 21, 21, 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: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724309 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000541724309 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724309/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724309/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541724309 Building ZINC000541725194 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541725194' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541725194 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541725194 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541725194/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541725194 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/883 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1nc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)ccc2o1) `ZINC000541725194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541725194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541725194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000541725194 none CN(C)c1nc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)ccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 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, 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] 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, 44, 44, 44, 44, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 1, 6, 6, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 11, 6, 6, 6, 6, 44, 44] 47 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541725194 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541725194/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541725194 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/884 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/884' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1nc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)ccc2o1) `ZINC000541725194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541725194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541725194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000541725194 none CN(C)c1nc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)ccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 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, 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] 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, 44, 44, 44, 44, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 1, 6, 6, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 11, 6, 6, 6, 6, 44, 44] 47 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541725194 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000541725194 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541725194/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541725194/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541725194 Building ZINC000541725194 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541725194' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541725194 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541725194 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541725194/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541725194 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 883) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN(C)c1nc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)ccc2o1) `ZINC000541725194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541725194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541725194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000541725194 none CN(C)c1nc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)ccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 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, 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] 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, 44, 44, 44, 44, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 1, 6, 6, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 11, 6, 6, 6, 6, 44, 44] 47 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541725194 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541725194/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541725194 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 884) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN(C)c1nc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)ccc2o1) `ZINC000541725194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541725194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541725194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000541725194 none CN(C)c1nc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)ccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 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, 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] 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, 44, 44, 44, 44, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 1, 6, 6, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 11, 6, 6, 6, 6, 44, 44] 47 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541725194 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000541725194 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541725194/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541725194/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541725194 Building ZINC000541726204 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541726204' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541726204 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541726204 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541726204/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541726204 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/885 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCc1nc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)ccc2o1) `ZINC000541726204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541726204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541726204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000541726204 none COCCc1nc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)ccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 12, 12, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 12, 12, 12, 50, 50, 50, 50, 50, 43, 43, 12, 2, 2, 2, 2, 2, 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]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541726204 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541726204/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541726204 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/886 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/886' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCc1nc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)ccc2o1) `ZINC000541726204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541726204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541726204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000541726204 none COCCc1nc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)ccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 12, 12, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 12, 50, 50, 50, 50, 50, 44, 44, 12, 2, 3, 3, 3, 3, 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]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541726204 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000541726204 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541726204/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541726204/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541726204 Building ZINC000541726204 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541726204' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541726204 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541726204 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541726204/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541726204 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 885) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COCCc1nc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)ccc2o1) `ZINC000541726204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541726204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541726204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000541726204 none COCCc1nc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)ccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 12, 12, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 12, 12, 12, 50, 50, 50, 50, 50, 43, 43, 12, 2, 2, 2, 2, 2, 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]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541726204 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541726204/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541726204 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 886) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COCCc1nc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)ccc2o1) `ZINC000541726204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541726204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541726204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000541726204 none COCCc1nc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)ccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 12, 12, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 12, 50, 50, 50, 50, 50, 44, 44, 12, 2, 3, 3, 3, 3, 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]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541726204 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000541726204 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541726204/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541726204/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541726204 Building ZINC000541730788 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730788' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730788 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541730788 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730788/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730788 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/887 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/887' -> `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)CCO1) `ZINC000541730788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541730788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000541730788 none Cc1ccccc1[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCO1 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', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 23, 23, 23, 23, 12, 2, 12, 1, 1, 1, 3, 3, 1, 2, 3, 3, 23, 23, 23, 49, 49, 49, 49, 49, 49, 49, 23, 23, 3, 3, 3, 3, 23, 23, 23, 23] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/83235/xao-8058115.15/working/building/ZINC000541730788 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730788/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730788 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/888 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/888' -> `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)CCO1) `ZINC000541730788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541730788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000541730788 none Cc1ccccc1[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCO1 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', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [48, 48, 48, 25, 48, 48, 21, 21, 21, 21, 12, 2, 12, 1, 1, 1, 4, 4, 1, 1, 4, 4, 21, 21, 21, 48, 48, 48, 48, 47, 48, 48, 21, 21, 4, 4, 4, 4, 21, 21, 21, 21] 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: 183 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730788 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000541730788 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730788/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730788/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730788 Building ZINC000541730788 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730788' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730788 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541730788 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730788/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730788 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 887) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccccc1[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCO1) `ZINC000541730788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541730788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000541730788 none Cc1ccccc1[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCO1 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', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 23, 23, 23, 23, 12, 2, 12, 1, 1, 1, 3, 3, 1, 2, 3, 3, 23, 23, 23, 49, 49, 49, 49, 49, 49, 49, 23, 23, 3, 3, 3, 3, 23, 23, 23, 23] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/83235/xao-8058115.15/working/building/ZINC000541730788 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730788/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730788 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 888) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccccc1[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCO1) `ZINC000541730788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541730788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000541730788 none Cc1ccccc1[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCO1 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', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [48, 48, 48, 25, 48, 48, 21, 21, 21, 21, 12, 2, 12, 1, 1, 1, 4, 4, 1, 1, 4, 4, 21, 21, 21, 48, 48, 48, 48, 47, 48, 48, 21, 21, 4, 4, 4, 4, 21, 21, 21, 21] 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: 183 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730788 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000541730788 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730788/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730788/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730788 Building ZINC000541730789 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730789' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730789 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541730789 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730789/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730789 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/889 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/889' -> `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)CCO1) `ZINC000541730789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541730789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000541730789 none Cc1ccccc1[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCO1 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', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [48, 48, 48, 48, 48, 48, 22, 22, 22, 22, 12, 2, 12, 1, 1, 1, 4, 4, 1, 1, 4, 4, 22, 22, 22, 48, 48, 48, 48, 48, 48, 48, 22, 22, 4, 4, 4, 4, 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]) total number of confs: 94 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730789 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730789/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730789 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/890 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/890' -> `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)CCO1) `ZINC000541730789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541730789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000541730789 none Cc1ccccc1[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCO1 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', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 12, 2, 12, 1, 1, 1, 2, 2, 1, 1, 2, 2, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 23, 23, 2, 2, 2, 2, 23, 23, 23, 23] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730789 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000541730789 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730789/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730789/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730789 Building ZINC000541730789 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730789' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730789 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541730789 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730789/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730789 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 889) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccccc1[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCO1) `ZINC000541730789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541730789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000541730789 none Cc1ccccc1[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCO1 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', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [48, 48, 48, 48, 48, 48, 22, 22, 22, 22, 12, 2, 12, 1, 1, 1, 4, 4, 1, 1, 4, 4, 22, 22, 22, 48, 48, 48, 48, 48, 48, 48, 22, 22, 4, 4, 4, 4, 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]) total number of confs: 94 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730789 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730789/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730789 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 890) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccccc1[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCO1) `ZINC000541730789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541730789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000541730789 none Cc1ccccc1[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCO1 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', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 12, 2, 12, 1, 1, 1, 2, 2, 1, 1, 2, 2, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 23, 23, 2, 2, 2, 2, 23, 23, 23, 23] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730789 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000541730789 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730789/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730789/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000541730789 Building ZINC000542512818 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542512818' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542512818 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542512818 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542512818/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542512818 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/891 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1ccc(OC(F)F)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542512818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542512818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542512818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000542512818 none O=C(NCCc1ccc(OC(F)F)cc1)[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', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 12, 5, 15, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 16, 16, 16, 16, 16, 45, 50, 50, 16, 16, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 8, 8, 16, 16, 16, 16, 50, 16, 16, 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]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542512818 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542512818/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542512818 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/892 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/892' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1ccc(OC(F)F)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542512818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542512818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542512818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000542512818 none O=C(NCCc1ccc(OC(F)F)cc1)[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', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 12, 5, 15, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 16, 16, 16, 16, 16, 45, 50, 50, 16, 16, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 8, 8, 16, 16, 16, 16, 50, 16, 16, 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]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542512818 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542512818 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542512818/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542512818/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542512818 Building ZINC000542512818 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542512818' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542512818 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542512818 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542512818/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542512818 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 891) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NCCc1ccc(OC(F)F)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542512818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542512818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542512818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000542512818 none O=C(NCCc1ccc(OC(F)F)cc1)[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', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 12, 5, 15, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 16, 16, 16, 16, 16, 45, 50, 50, 16, 16, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 8, 8, 16, 16, 16, 16, 50, 16, 16, 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]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542512818 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542512818/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542512818 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 892) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NCCc1ccc(OC(F)F)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542512818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542512818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542512818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000542512818 none O=C(NCCc1ccc(OC(F)F)cc1)[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', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 12, 5, 15, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 16, 16, 16, 16, 16, 45, 50, 50, 16, 16, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 8, 8, 16, 16, 16, 16, 50, 16, 16, 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]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542512818 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542512818 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542512818/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542512818/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542512818 Building ZINC000542513303 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542513303' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542513303 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542513303 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542513303/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542513303 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/893 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1ncc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cnc21) `ZINC000542513303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542513303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542513303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000542513303 none CC(C)n1ncc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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, 28, 50, 28, 28, 28, 28, 28, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 2, 5, 5, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 28, 28, 4, 5, 5, 5, 5, 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]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542513303 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542513303/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542513303 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/894 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/894' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1ncc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cnc21) `ZINC000542513303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542513303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542513303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000542513303 none CC(C)n1ncc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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, 26, 49, 26, 26, 26, 26, 26, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 26, 26, 26, 49, 49, 49, 49, 49, 49, 49, 26, 26, 4, 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, 36, 37, 38]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542513303 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542513303 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542513303/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542513303/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542513303 Building ZINC000542513303 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542513303' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542513303 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542513303 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542513303/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542513303 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 893) grep: /scratch/xiaobo/83235/xao-8058115.15/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)n1ncc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cnc21) `ZINC000542513303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542513303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542513303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000542513303 none CC(C)n1ncc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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, 28, 50, 28, 28, 28, 28, 28, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 2, 5, 5, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 28, 28, 4, 5, 5, 5, 5, 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]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542513303 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542513303/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542513303 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 894) grep: /scratch/xiaobo/83235/xao-8058115.15/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)n1ncc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cnc21) `ZINC000542513303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542513303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542513303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000542513303 none CC(C)n1ncc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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, 26, 49, 26, 26, 26, 26, 26, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 26, 26, 26, 49, 49, 49, 49, 49, 49, 49, 26, 26, 4, 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, 36, 37, 38]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542513303 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542513303 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542513303/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542513303/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542513303 Building ZINC000444045750 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045750' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045750 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000444045750 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045750/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045750 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/895 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@]1(O)CCC[C@@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000444045750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000444045750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000444045750 none O=C(NC[C@]1(O)CCC[C@@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 4, 19, 19, 150, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 150 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: 309 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045750 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045750/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045750 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/896 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/896' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@]1(O)CCC[C@@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000444045750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000444045750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000444045750 none O=C(NC[C@]1(O)CCC[C@@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 17, 17, 150, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 150 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: 304 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045750 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000444045750 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045750/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045750/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045750 Building ZINC000444045750 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045750' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045750 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000444045750 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045750/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045750 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 895) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NC[C@]1(O)CCC[C@@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000444045750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000444045750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000444045750 none O=C(NC[C@]1(O)CCC[C@@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 4, 19, 19, 150, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 150 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: 309 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045750 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045750/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045750 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 896) grep: /scratch/xiaobo/83235/xao-8058115.15/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(NC[C@]1(O)CCC[C@@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000444045750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000444045750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000444045750 none O=C(NC[C@]1(O)CCC[C@@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 17, 17, 150, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 150 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: 304 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045750 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000444045750 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045750/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045750/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045750 Building ZINC000444045752 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045752' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045752 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000444045752 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045752/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045752 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/897 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@]1(O)CCC[C@@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000444045752.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000444045752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000444045752 none O=C(NC[C@@]1(O)CCC[C@@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 25, 50, 46, 50, 50, 50, 50, 46, 50, 50, 50, 46, 1, 1, 1, 3, 3, 1, 1, 3, 3, 5, 25, 25, 150, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 150 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: 382 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045752 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045752/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045752 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/898 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/898' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@]1(O)CCC[C@@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000444045752.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000444045752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045752/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000444045752 none O=C(NC[C@@]1(O)CCC[C@@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 22, 50, 48, 50, 50, 50, 50, 47, 50, 50, 50, 47, 1, 1, 1, 4, 4, 1, 1, 4, 4, 5, 22, 22, 150, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 150 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: 361 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045752 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000444045752 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045752/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045752/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045752 Building ZINC000444045752 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045752' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045752 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000444045752 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045752/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045752 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 897) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@@]1(O)CCC[C@@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000444045752.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000444045752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000444045752 none O=C(NC[C@@]1(O)CCC[C@@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 25, 50, 46, 50, 50, 50, 50, 46, 50, 50, 50, 46, 1, 1, 1, 3, 3, 1, 1, 3, 3, 5, 25, 25, 150, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 150 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: 382 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045752 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045752/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045752 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 898) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@@]1(O)CCC[C@@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000444045752.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000444045752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045752/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000444045752 none O=C(NC[C@@]1(O)CCC[C@@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 22, 50, 48, 50, 50, 50, 50, 47, 50, 50, 50, 47, 1, 1, 1, 4, 4, 1, 1, 4, 4, 5, 22, 22, 150, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 150 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: 361 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045752 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000444045752 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045752/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045752/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045752 Building ZINC000444045754 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045754' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045754 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000444045754 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045754/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045754 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/899 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@]1(O)CCC[C@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000444045754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000444045754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000444045754 none O=C(NC[C@]1(O)CCC[C@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 5, 23, 23, 150, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 150 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: 313 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045754 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045754/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045754 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/900 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/900' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@]1(O)CCC[C@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000444045754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000444045754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000444045754 none O=C(NC[C@]1(O)CCC[C@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 22, 22, 150, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 150 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: 310 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045754 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000444045754 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045754/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045754/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045754 Building ZINC000444045754 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045754' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045754 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000444045754 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045754/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045754 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 899) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@]1(O)CCC[C@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000444045754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000444045754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000444045754 none O=C(NC[C@]1(O)CCC[C@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 5, 23, 23, 150, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 150 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: 313 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045754 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045754/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045754 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 900) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@]1(O)CCC[C@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000444045754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000444045754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000444045754 none O=C(NC[C@]1(O)CCC[C@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 22, 22, 150, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 150 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: 310 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045754 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000444045754 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045754/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045754/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045754 Building ZINC000444045756 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045756' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045756 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000444045756 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045756/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045756 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/901 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@]1(O)CCC[C@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000444045756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000444045756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000444045756 none O=C(NC[C@@]1(O)CCC[C@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 15, 15, 150, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 150 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: 279 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045756 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045756/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045756 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/902 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/902' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@]1(O)CCC[C@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000444045756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000444045756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000444045756 none O=C(NC[C@@]1(O)CCC[C@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 3, 3, 3, 3, 4, 16, 16, 150, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 150 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: 292 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045756 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000444045756 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045756/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045756/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045756 Building ZINC000444045756 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045756' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045756 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000444045756 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045756/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045756 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 901) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@@]1(O)CCC[C@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000444045756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000444045756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000444045756 none O=C(NC[C@@]1(O)CCC[C@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 15, 15, 150, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 150 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: 279 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045756 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045756/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045756 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 902) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC[C@@]1(O)CCC[C@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000444045756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000444045756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000444045756 none O=C(NC[C@@]1(O)CCC[C@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 3, 3, 3, 3, 4, 16, 16, 150, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 150 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: 292 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045756 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000444045756 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045756/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045756/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444045756 Building ZINC000542549634 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542549634' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542549634 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542549634 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542549634/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542549634 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/903 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(c2ccccc2)CCOCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542549634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542549634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542549634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000542549634 none O=C(NC1(c2ccccc2)CCOCC1)[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.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 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, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 10, 36, 47, 47, 39, 47, 47, 36, 36, 36, 36, 36, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 47, 47, 47, 47, 47, 36, 36, 36, 36, 36, 36, 36, 36, 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: 159 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542549634 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542549634/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542549634 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/904 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/904' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(c2ccccc2)CCOCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542549634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542549634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542549634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000542549634 none O=C(NC1(c2ccccc2)CCOCC1)[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.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 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, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 10, 36, 46, 46, 36, 46, 46, 36, 36, 36, 36, 36, 1, 1, 1, 5, 5, 1, 1, 5, 5, 7, 46, 46, 36, 46, 46, 36, 36, 36, 36, 36, 36, 36, 36, 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: 142 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542549634 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542549634 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542549634/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542549634/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542549634 Building ZINC000542549634 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542549634' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542549634 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542549634 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542549634/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542549634 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 903) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC1(c2ccccc2)CCOCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542549634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542549634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542549634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000542549634 none O=C(NC1(c2ccccc2)CCOCC1)[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.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 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, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 10, 36, 47, 47, 39, 47, 47, 36, 36, 36, 36, 36, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 47, 47, 47, 47, 47, 36, 36, 36, 36, 36, 36, 36, 36, 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: 159 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542549634 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542549634/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542549634 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 904) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(NC1(c2ccccc2)CCOCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542549634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542549634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542549634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000542549634 none O=C(NC1(c2ccccc2)CCOCC1)[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.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 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, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 10, 36, 46, 46, 36, 46, 46, 36, 36, 36, 36, 36, 1, 1, 1, 5, 5, 1, 1, 5, 5, 7, 46, 46, 36, 46, 46, 36, 36, 36, 36, 36, 36, 36, 36, 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: 142 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542549634 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542549634 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542549634/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542549634/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542549634 Building ZINC000542650648 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542650648' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542650648 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542650648 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542650648/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542650648 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/905 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(C(=O)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000542650648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542650648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542650648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000542650648 none CCCOc1ccc(C(=O)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.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.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, 12, 1, 1, 1, 1, 1, 11, 5, 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, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 27, 27, 27, 27, 15, 10, 15, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 27, 50, 50, 50, 50, 50, 48, 48, 27, 27, 10, 10, 2, 2, 2, 2, 2, 27, 27] 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: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542650648 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542650648/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542650648 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/906 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/906' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(C(=O)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000542650648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542650648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542650648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000542650648 none CCCOc1ccc(C(=O)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.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.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, 12, 1, 1, 1, 1, 1, 11, 5, 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, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 27, 15, 27, 27, 15, 10, 15, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 27, 50, 50, 50, 50, 50, 47, 47, 27, 27, 10, 10, 2, 2, 2, 2, 2, 27, 27] 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: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542650648 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542650648 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542650648/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542650648/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542650648 Building ZINC000542650648 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542650648' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542650648 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542650648 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542650648/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542650648 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 905) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCCOc1ccc(C(=O)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000542650648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542650648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542650648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000542650648 none CCCOc1ccc(C(=O)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.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.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, 12, 1, 1, 1, 1, 1, 11, 5, 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, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 27, 27, 27, 27, 15, 10, 15, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 27, 50, 50, 50, 50, 50, 48, 48, 27, 27, 10, 10, 2, 2, 2, 2, 2, 27, 27] 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: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542650648 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542650648/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542650648 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 906) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCCOc1ccc(C(=O)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000542650648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542650648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542650648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000542650648 none CCCOc1ccc(C(=O)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.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.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, 12, 1, 1, 1, 1, 1, 11, 5, 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, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 27, 15, 27, 27, 15, 10, 15, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 27, 50, 50, 50, 50, 50, 47, 47, 27, 27, 10, 10, 2, 2, 2, 2, 2, 27, 27] 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: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542650648 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542650648 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542650648/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542650648/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542650648 Building ZINC000542651282 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651282' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651282 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542651282 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651282/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651282 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/907 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](O)CN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542651282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542651282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000542651282 none CC[C@H](O)CN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 21, 13, 22, 22, 7, 4, 7, 20, 26, 26, 26, 26, 26, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 26, 26, 66, 13, 13, 20, 20, 26, 26, 26, 26, 26, 3, 3, 3, 3] 150 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: 259 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651282 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651282/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651282 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/908 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/908' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](O)CN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542651282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542651282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000542651282 none CC[C@H](O)CN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 23, 11, 23, 23, 6, 2, 6, 16, 21, 21, 17, 21, 21, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 29, 29, 69, 11, 11, 16, 16, 21, 21, 21, 21, 21, 3, 3, 3, 3] 150 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: 282 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651282 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542651282 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651282/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651282/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651282 Building ZINC000542651282 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651282' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651282 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542651282 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651282/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651282 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 907) grep: /scratch/xiaobo/83235/xao-8058115.15/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@H](O)CN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542651282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542651282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000542651282 none CC[C@H](O)CN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 21, 13, 22, 22, 7, 4, 7, 20, 26, 26, 26, 26, 26, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 26, 26, 66, 13, 13, 20, 20, 26, 26, 26, 26, 26, 3, 3, 3, 3] 150 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: 259 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651282 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651282/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651282 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 908) grep: /scratch/xiaobo/83235/xao-8058115.15/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@H](O)CN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542651282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542651282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000542651282 none CC[C@H](O)CN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 23, 11, 23, 23, 6, 2, 6, 16, 21, 21, 17, 21, 21, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 29, 29, 69, 11, 11, 16, 16, 21, 21, 21, 21, 21, 3, 3, 3, 3] 150 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: 282 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651282 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542651282 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651282/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651282/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651282 Building ZINC000542651283 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651283' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651283 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542651283 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651283/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651283 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/909 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](O)CN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542651283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542651283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000542651283 none CC[C@@H](O)CN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 24, 12, 24, 24, 7, 3, 7, 17, 23, 23, 20, 23, 23, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 30, 72, 12, 12, 17, 17, 23, 23, 23, 23, 23, 3, 3, 3, 3] 150 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: 281 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651283 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651283/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651283 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/910 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/910' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](O)CN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542651283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542651283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000542651283 none CC[C@@H](O)CN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 23, 12, 23, 23, 6, 3, 6, 19, 24, 24, 21, 24, 24, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 27, 27, 69, 12, 12, 19, 19, 24, 24, 24, 24, 24, 3, 3, 3, 3] 150 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: 277 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651283 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542651283 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651283/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651283/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651283 Building ZINC000542651283 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651283' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651283 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542651283 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651283/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651283 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 909) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC[C@@H](O)CN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542651283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542651283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000542651283 none CC[C@@H](O)CN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 24, 12, 24, 24, 7, 3, 7, 17, 23, 23, 20, 23, 23, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 30, 72, 12, 12, 17, 17, 23, 23, 23, 23, 23, 3, 3, 3, 3] 150 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: 281 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651283 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651283/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651283 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 910) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC[C@@H](O)CN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542651283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542651283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000542651283 none CC[C@@H](O)CN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 23, 12, 23, 23, 6, 3, 6, 19, 24, 24, 21, 24, 24, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 27, 27, 69, 12, 12, 19, 19, 24, 24, 24, 24, 24, 3, 3, 3, 3] 150 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: 277 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651283 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542651283 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651283/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651283/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542651283 Building ZINC000542652719 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652719' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652719 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542652719 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652719/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652719 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/911 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1) `ZINC000542652719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542652719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000542652719 none C[C@H](O)C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 47, 48, 48, 34, 19, 34, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 34, 42, 42, 34, 42, 42, 48, 48, 48, 144, 47, 47, 19, 19, 4, 3, 3, 3, 3, 42, 42, 34, 42, 42] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 407 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652719 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652719/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652719 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/912 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/912' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1) `ZINC000542652719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542652719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000542652719 none C[C@H](O)C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 32, 17, 33, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 41, 41, 33, 41, 41, 45, 45, 45, 135, 45, 45, 17, 17, 3, 3, 3, 3, 3, 41, 41, 33, 41, 41] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 386 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652719 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542652719 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652719/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652719/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652719 Building ZINC000542652719 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652719' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652719 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542652719 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652719/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652719 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 911) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H](O)C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1) `ZINC000542652719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542652719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000542652719 none C[C@H](O)C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 47, 48, 48, 34, 19, 34, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 34, 42, 42, 34, 42, 42, 48, 48, 48, 144, 47, 47, 19, 19, 4, 3, 3, 3, 3, 42, 42, 34, 42, 42] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 407 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652719 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652719/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652719 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 912) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H](O)C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1) `ZINC000542652719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542652719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000542652719 none C[C@H](O)C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 32, 17, 33, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 41, 41, 33, 41, 41, 45, 45, 45, 135, 45, 45, 17, 17, 3, 3, 3, 3, 3, 41, 41, 33, 41, 41] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 386 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652719 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542652719 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652719/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652719/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652719 Building ZINC000542652720 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652720' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652720 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542652720 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652720/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652720 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/913 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1) `ZINC000542652720.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542652720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000542652720 none C[C@@H](O)C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [46, 40, 46, 46, 32, 17, 32, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 32, 38, 38, 32, 38, 38, 46, 46, 46, 138, 40, 40, 17, 17, 4, 3, 3, 3, 3, 38, 38, 32, 38, 38] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 388 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652720 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652720/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652720 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/914 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/914' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1) `ZINC000542652720.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542652720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652720/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000542652720 none C[C@@H](O)C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [46, 39, 46, 46, 33, 18, 33, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 40, 40, 33, 40, 40, 46, 46, 46, 138, 39, 39, 18, 18, 4, 3, 3, 3, 3, 40, 40, 33, 40, 40] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 393 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652720 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542652720 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652720/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652720/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652720 Building ZINC000542652720 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652720' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652720 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542652720 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652720/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652720 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 913) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H](O)C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1) `ZINC000542652720.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542652720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000542652720 none C[C@@H](O)C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [46, 40, 46, 46, 32, 17, 32, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 32, 38, 38, 32, 38, 38, 46, 46, 46, 138, 40, 40, 17, 17, 4, 3, 3, 3, 3, 38, 38, 32, 38, 38] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 388 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652720 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652720/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652720 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 914) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H](O)C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1) `ZINC000542652720.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542652720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652720/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000542652720 none C[C@@H](O)C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [46, 39, 46, 46, 33, 18, 33, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 40, 40, 33, 40, 40, 46, 46, 46, 138, 39, 39, 18, 18, 4, 3, 3, 3, 3, 40, 40, 33, 40, 40] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 393 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652720 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542652720 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652720/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652720/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652720 Building ZINC000542652721 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652721' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652721 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542652721 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652721/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652721 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/915 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1) `ZINC000542652721.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542652721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000542652721 none C[C@@H](O)C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 46, 32, 17, 33, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 41, 41, 33, 41, 41, 46, 46, 46, 138, 46, 46, 17, 17, 3, 3, 3, 3, 3, 41, 41, 33, 41, 41] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 392 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652721 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652721/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652721 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/916 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/916' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1) `ZINC000542652721.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542652721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000542652721 none C[C@@H](O)C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 47, 34, 19, 34, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 34, 42, 42, 34, 42, 42, 47, 47, 47, 141, 47, 47, 19, 19, 4, 3, 3, 3, 3, 42, 42, 34, 42, 42] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 398 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652721 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542652721 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652721/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652721/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652721 Building ZINC000542652721 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652721' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652721 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542652721 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652721/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652721 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 915) grep: /scratch/xiaobo/83235/xao-8058115.15/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](O)C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1) `ZINC000542652721.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542652721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000542652721 none C[C@@H](O)C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 46, 32, 17, 33, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 41, 41, 33, 41, 41, 46, 46, 46, 138, 46, 46, 17, 17, 3, 3, 3, 3, 3, 41, 41, 33, 41, 41] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 392 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652721 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652721/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652721 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 916) grep: /scratch/xiaobo/83235/xao-8058115.15/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](O)C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1) `ZINC000542652721.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542652721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000542652721 none C[C@@H](O)C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 47, 34, 19, 34, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 34, 42, 42, 34, 42, 42, 47, 47, 47, 141, 47, 47, 19, 19, 4, 3, 3, 3, 3, 42, 42, 34, 42, 42] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 398 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652721 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542652721 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652721/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652721/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652721 Building ZINC000542652722 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652722' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652722 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542652722 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652722/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652722 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/917 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1) `ZINC000542652722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542652722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000542652722 none C[C@H](O)C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 38, 45, 45, 30, 15, 30, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 37, 37, 30, 37, 37, 45, 45, 45, 135, 38, 38, 15, 15, 3, 3, 3, 3, 3, 37, 37, 30, 37, 37] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 388 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652722 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652722/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652722 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/918 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/918' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1) `ZINC000542652722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542652722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000542652722 none C[C@H](O)C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [46, 40, 46, 46, 32, 17, 32, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 32, 38, 38, 32, 38, 38, 46, 46, 46, 138, 40, 40, 17, 17, 4, 3, 3, 3, 3, 38, 38, 32, 38, 38] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 388 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652722 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542652722 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652722/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652722/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652722 Building ZINC000542652722 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652722' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652722 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542652722 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652722/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652722 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 917) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H](O)C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1) `ZINC000542652722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542652722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000542652722 none C[C@H](O)C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 38, 45, 45, 30, 15, 30, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 37, 37, 30, 37, 37, 45, 45, 45, 135, 38, 38, 15, 15, 3, 3, 3, 3, 3, 37, 37, 30, 37, 37] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 388 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652722 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652722/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652722 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 918) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H](O)C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1) `ZINC000542652722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542652722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000542652722 none C[C@H](O)C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [46, 40, 46, 46, 32, 17, 32, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 32, 38, 38, 32, 38, 38, 46, 46, 46, 138, 40, 40, 17, 17, 4, 3, 3, 3, 3, 38, 38, 32, 38, 38] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 388 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652722 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542652722 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652722/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652722/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542652722 Building ZINC000542653215 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653215' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653215 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542653215 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653215/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653215 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/919 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)c1ccc(F)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542653215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542653215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000542653215 none C[C@H](CC(=O)c1ccc(F)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 5, 1, 11, 1, 1, 1, 1, 15, 1, 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, 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] 0 hydrogens 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, 10, 22, 40, 40, 50, 50, 40, 40, 50, 50, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 22, 22, 50, 50, 50, 50, 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]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653215 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653215/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653215 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/920 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/920' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)c1ccc(F)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542653215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542653215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000542653215 none C[C@H](CC(=O)c1ccc(F)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 5, 1, 11, 1, 1, 1, 1, 15, 1, 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, 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] 0 hydrogens 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, 9, 23, 44, 44, 50, 50, 44, 50, 50, 50, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 9, 23, 23, 50, 50, 50, 50, 3, 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]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653215 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542653215 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653215/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653215/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653215 Building ZINC000542653215 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653215' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653215 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542653215 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653215/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653215 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 919) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/919: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)c1ccc(F)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542653215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542653215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000542653215 none C[C@H](CC(=O)c1ccc(F)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 5, 1, 11, 1, 1, 1, 1, 15, 1, 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, 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] 0 hydrogens 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, 10, 22, 40, 40, 50, 50, 40, 40, 50, 50, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 22, 22, 50, 50, 50, 50, 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]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653215 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653215/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653215 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 920) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/920: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)c1ccc(F)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542653215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542653215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000542653215 none C[C@H](CC(=O)c1ccc(F)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 5, 1, 11, 1, 1, 1, 1, 15, 1, 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, 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] 0 hydrogens 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, 9, 23, 44, 44, 50, 50, 44, 50, 50, 50, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 9, 23, 23, 50, 50, 50, 50, 3, 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]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653215 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542653215 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653215/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653215/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653215 Building ZINC000542653216 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653216' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653216 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542653216 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653216/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653216 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/921 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)c1ccc(F)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542653216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542653216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000542653216 none C[C@@H](CC(=O)c1ccc(F)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 5, 1, 11, 1, 1, 1, 1, 15, 1, 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, 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] 0 hydrogens 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, 9, 23, 44, 44, 50, 50, 44, 50, 50, 50, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 9, 23, 23, 50, 50, 50, 50, 3, 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]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653216 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653216/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653216 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/922 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/922' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)c1ccc(F)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542653216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542653216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000542653216 none C[C@@H](CC(=O)c1ccc(F)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 5, 1, 11, 1, 1, 1, 1, 15, 1, 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, 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] 0 hydrogens 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, 10, 22, 40, 40, 50, 50, 40, 48, 50, 50, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 22, 22, 50, 50, 50, 50, 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]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653216 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542653216 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653216/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653216/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653216 Building ZINC000542653216 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653216' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653216 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542653216 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653216/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653216 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 921) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H](CC(=O)c1ccc(F)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542653216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542653216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000542653216 none C[C@@H](CC(=O)c1ccc(F)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 5, 1, 11, 1, 1, 1, 1, 15, 1, 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, 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] 0 hydrogens 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, 9, 23, 44, 44, 50, 50, 44, 50, 50, 50, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 9, 23, 23, 50, 50, 50, 50, 3, 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]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653216 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653216/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653216 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 922) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H](CC(=O)c1ccc(F)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542653216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542653216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000542653216 none C[C@@H](CC(=O)c1ccc(F)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 5, 1, 11, 1, 1, 1, 1, 15, 1, 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, 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] 0 hydrogens 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, 10, 22, 40, 40, 50, 50, 40, 48, 50, 50, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 22, 22, 50, 50, 50, 50, 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]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653216 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542653216 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653216/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653216/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542653216 Building ZINC000542656380 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000542656380 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/923 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542656380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656380 none C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 29, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 43, 50, 50, 43, 50, 50, 29, 29, 29, 29, 29, 2, 3, 3, 3, 3, 29, 29, 43, 43, 50, 50, 43, 50, 50] 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, 45]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/924 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/924' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542656380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656380 none C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 29, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 43, 50, 50, 43, 50, 50, 29, 29, 29, 29, 29, 2, 3, 3, 3, 3, 29, 29, 43, 43, 50, 50, 43, 50, 50] 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, 45]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/925 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/925' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656380.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000542656380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656380 none C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 32, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 32, 32, 32, 45, 50, 50, 45, 50, 50, 32, 32, 32, 32, 32, 3, 3, 3, 3, 3, 32, 32, 45, 45, 50, 50, 45, 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, 43, 44, 45]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/926 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/926' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656380.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000542656380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656380 none C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 32, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 32, 32, 32, 45, 50, 50, 45, 50, 50, 32, 32, 32, 32, 32, 3, 3, 3, 3, 3, 32, 32, 45, 45, 50, 50, 45, 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, 43, 44, 45]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542656380 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 Building ZINC000542656380 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000542656380 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 923) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/923: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542656380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656380 none C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 29, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 43, 50, 50, 43, 50, 50, 29, 29, 29, 29, 29, 2, 3, 3, 3, 3, 29, 29, 43, 43, 50, 50, 43, 50, 50] 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, 45]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 924) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/924: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542656380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656380 none C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 29, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 43, 50, 50, 43, 50, 50, 29, 29, 29, 29, 29, 2, 3, 3, 3, 3, 29, 29, 43, 43, 50, 50, 43, 50, 50] 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, 45]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 925) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/925: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656380.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000542656380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656380 none C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 32, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 32, 32, 32, 45, 50, 50, 45, 50, 50, 32, 32, 32, 32, 32, 3, 3, 3, 3, 3, 32, 32, 45, 45, 50, 50, 45, 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, 43, 44, 45]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 926) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/926: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656380.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000542656380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656380 none C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 32, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 32, 32, 32, 45, 50, 50, 45, 50, 50, 32, 32, 32, 32, 32, 3, 3, 3, 3, 3, 32, 32, 45, 45, 50, 50, 45, 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, 43, 44, 45]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542656380 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 Building ZINC000542656380 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000542656380 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 923) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/923: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542656380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656380 none C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 29, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 43, 50, 50, 43, 50, 50, 29, 29, 29, 29, 29, 2, 3, 3, 3, 3, 29, 29, 43, 43, 50, 50, 43, 50, 50] 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, 45]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 924) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/924: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542656380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656380 none C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 29, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 43, 50, 50, 43, 50, 50, 29, 29, 29, 29, 29, 2, 3, 3, 3, 3, 29, 29, 43, 43, 50, 50, 43, 50, 50] 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, 45]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 925) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/925: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656380.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000542656380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656380 none C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 32, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 32, 32, 32, 45, 50, 50, 45, 50, 50, 32, 32, 32, 32, 32, 3, 3, 3, 3, 3, 32, 32, 45, 45, 50, 50, 45, 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, 43, 44, 45]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 926) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/926: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656380.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000542656380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656380 none C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 32, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 32, 32, 32, 45, 50, 50, 45, 50, 50, 32, 32, 32, 32, 32, 3, 3, 3, 3, 3, 32, 32, 45, 45, 50, 50, 45, 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, 43, 44, 45]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542656380 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 Building ZINC000542656380 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000542656380 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 923) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/923: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542656380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656380 none C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 29, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 43, 50, 50, 43, 50, 50, 29, 29, 29, 29, 29, 2, 3, 3, 3, 3, 29, 29, 43, 43, 50, 50, 43, 50, 50] 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, 45]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 924) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/924: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542656380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656380 none C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 29, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 43, 50, 50, 43, 50, 50, 29, 29, 29, 29, 29, 2, 3, 3, 3, 3, 29, 29, 43, 43, 50, 50, 43, 50, 50] 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, 45]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 925) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/925: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656380.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000542656380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656380 none C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 32, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 32, 32, 32, 45, 50, 50, 45, 50, 50, 32, 32, 32, 32, 32, 3, 3, 3, 3, 3, 32, 32, 45, 45, 50, 50, 45, 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, 43, 44, 45]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 926) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/926: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656380.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000542656380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656380 none C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 32, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 32, 32, 32, 45, 50, 50, 45, 50, 50, 32, 32, 32, 32, 32, 3, 3, 3, 3, 3, 32, 32, 45, 45, 50, 50, 45, 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, 43, 44, 45]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542656380 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656380 Building ZINC000542656381 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000542656381 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/927 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542656381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656381 none C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 29, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 42, 50, 50, 48, 50, 50, 29, 29, 29, 29, 29, 4, 3, 3, 3, 3, 29, 29, 42, 42, 50, 50, 48, 50, 50] 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, 45]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/928 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/928' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542656381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656381 none C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 29, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 42, 50, 50, 48, 50, 50, 29, 29, 29, 29, 29, 4, 3, 3, 3, 3, 29, 29, 42, 42, 50, 50, 48, 50, 50] 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, 45]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/929 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/929' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656381.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000542656381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656381 none C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 28, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 43, 50, 50, 44, 50, 50, 28, 28, 28, 28, 28, 4, 3, 3, 3, 3, 28, 28, 43, 43, 50, 50, 44, 50, 50] 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, 45]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/930 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/930' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656381.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000542656381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656381 none C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 28, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 43, 50, 50, 44, 50, 50, 28, 28, 28, 28, 28, 4, 3, 3, 3, 3, 28, 28, 43, 43, 50, 50, 44, 50, 50] 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, 45]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542656381 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 Building ZINC000542656381 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000542656381 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 927) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542656381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656381 none C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 29, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 42, 50, 50, 48, 50, 50, 29, 29, 29, 29, 29, 4, 3, 3, 3, 3, 29, 29, 42, 42, 50, 50, 48, 50, 50] 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, 45]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 928) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542656381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656381 none C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 29, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 42, 50, 50, 48, 50, 50, 29, 29, 29, 29, 29, 4, 3, 3, 3, 3, 29, 29, 42, 42, 50, 50, 48, 50, 50] 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, 45]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 929) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/929: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656381.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000542656381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656381 none C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 28, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 43, 50, 50, 44, 50, 50, 28, 28, 28, 28, 28, 4, 3, 3, 3, 3, 28, 28, 43, 43, 50, 50, 44, 50, 50] 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, 45]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 930) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/930: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656381.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000542656381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656381 none C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 28, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 43, 50, 50, 44, 50, 50, 28, 28, 28, 28, 28, 4, 3, 3, 3, 3, 28, 28, 43, 43, 50, 50, 44, 50, 50] 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, 45]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542656381 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 Building ZINC000542656381 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000542656381 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 927) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542656381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656381 none C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 29, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 42, 50, 50, 48, 50, 50, 29, 29, 29, 29, 29, 4, 3, 3, 3, 3, 29, 29, 42, 42, 50, 50, 48, 50, 50] 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, 45]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 928) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542656381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656381 none C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 29, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 42, 50, 50, 48, 50, 50, 29, 29, 29, 29, 29, 4, 3, 3, 3, 3, 29, 29, 42, 42, 50, 50, 48, 50, 50] 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, 45]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 929) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/929: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656381.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000542656381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656381 none C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 28, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 43, 50, 50, 44, 50, 50, 28, 28, 28, 28, 28, 4, 3, 3, 3, 3, 28, 28, 43, 43, 50, 50, 44, 50, 50] 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, 45]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 930) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/930: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656381.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000542656381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656381 none C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 28, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 43, 50, 50, 44, 50, 50, 28, 28, 28, 28, 28, 4, 3, 3, 3, 3, 28, 28, 43, 43, 50, 50, 44, 50, 50] 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, 45]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542656381 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 Building ZINC000542656381 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000542656381 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 927) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542656381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656381 none C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 29, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 42, 50, 50, 48, 50, 50, 29, 29, 29, 29, 29, 4, 3, 3, 3, 3, 29, 29, 42, 42, 50, 50, 48, 50, 50] 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, 45]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 928) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542656381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656381 none C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 29, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 42, 50, 50, 48, 50, 50, 29, 29, 29, 29, 29, 4, 3, 3, 3, 3, 29, 29, 42, 42, 50, 50, 48, 50, 50] 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, 45]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 929) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/929: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656381.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000542656381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656381 none C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 28, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 43, 50, 50, 44, 50, 50, 28, 28, 28, 28, 28, 4, 3, 3, 3, 3, 28, 28, 43, 43, 50, 50, 44, 50, 50] 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, 45]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 930) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/930: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656381.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000542656381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656381 none C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 28, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 43, 50, 50, 44, 50, 50, 28, 28, 28, 28, 28, 4, 3, 3, 3, 3, 28, 28, 43, 43, 50, 50, 44, 50, 50] 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, 45]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542656381 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656381 Building ZINC000542656382 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000542656382 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/931 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542656382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656382 none C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 26, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 43, 50, 50, 44, 50, 50, 26, 26, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 43, 43, 50, 50, 44, 50, 50] 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, 45]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/932 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/932' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542656382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656382 none C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 26, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 43, 50, 50, 44, 50, 50, 26, 26, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 43, 43, 50, 50, 44, 50, 50] 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, 45]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/933 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/933' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656382.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000542656382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656382 none C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 26, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 44, 50, 50, 45, 50, 50, 26, 26, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 44, 44, 50, 50, 45, 50, 50] 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, 45]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/934 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/934' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656382.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000542656382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656382 none C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 26, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 44, 50, 50, 45, 50, 50, 26, 26, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 44, 44, 50, 50, 45, 50, 50] 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, 45]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542656382 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 Building ZINC000542656382 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000542656382 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 931) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542656382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656382 none C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 26, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 43, 50, 50, 44, 50, 50, 26, 26, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 43, 43, 50, 50, 44, 50, 50] 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, 45]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 932) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542656382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656382 none C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 26, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 43, 50, 50, 44, 50, 50, 26, 26, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 43, 43, 50, 50, 44, 50, 50] 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, 45]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 933) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/933: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656382.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000542656382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656382 none C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 26, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 44, 50, 50, 45, 50, 50, 26, 26, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 44, 44, 50, 50, 45, 50, 50] 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, 45]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 934) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656382.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000542656382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656382 none C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 26, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 44, 50, 50, 45, 50, 50, 26, 26, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 44, 44, 50, 50, 45, 50, 50] 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, 45]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542656382 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 Building ZINC000542656382 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000542656382 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 931) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542656382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656382 none C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 26, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 43, 50, 50, 44, 50, 50, 26, 26, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 43, 43, 50, 50, 44, 50, 50] 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, 45]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 932) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542656382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656382 none C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 26, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 43, 50, 50, 44, 50, 50, 26, 26, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 43, 43, 50, 50, 44, 50, 50] 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, 45]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 933) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/933: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656382.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000542656382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656382 none C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 26, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 44, 50, 50, 45, 50, 50, 26, 26, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 44, 44, 50, 50, 45, 50, 50] 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, 45]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 934) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656382.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000542656382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656382 none C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 26, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 44, 50, 50, 45, 50, 50, 26, 26, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 44, 44, 50, 50, 45, 50, 50] 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, 45]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542656382 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 Building ZINC000542656382 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000542656382 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 931) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542656382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656382 none C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 26, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 43, 50, 50, 44, 50, 50, 26, 26, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 43, 43, 50, 50, 44, 50, 50] 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, 45]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 932) grep: /scratch/xiaobo/83235/xao-8058115.15/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: C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542656382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656382 none C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 26, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 43, 50, 50, 44, 50, 50, 26, 26, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 43, 43, 50, 50, 44, 50, 50] 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, 45]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 933) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/933: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656382.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000542656382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656382 none C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 26, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 44, 50, 50, 45, 50, 50, 26, 26, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 44, 44, 50, 50, 45, 50, 50] 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, 45]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 934) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656382.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000542656382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656382 none C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 26, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 44, 50, 50, 45, 50, 50, 26, 26, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 44, 44, 50, 50, 45, 50, 50] 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, 45]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542656382 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656382 Building ZINC000542656383 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000542656383 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/935 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656383.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542656383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656383 none C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 18, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 44, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 44, 44, 50, 50, 50, 50, 50] 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, 45]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/936 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/936' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656383.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542656383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656383 none C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 18, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 44, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 44, 44, 50, 50, 50, 50, 50] 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, 45]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/937 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/937' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656383.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000542656383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656383 none C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 18, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 42, 50, 50, 49, 50, 50, 25, 25, 25, 25, 25, 3, 3, 3, 3, 3, 25, 25, 42, 42, 50, 50, 49, 50, 50] 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, 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/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/938 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/938' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656383.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000542656383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656383 none C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 18, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 42, 50, 50, 49, 50, 50, 25, 25, 25, 25, 25, 3, 3, 3, 3, 3, 25, 25, 42, 42, 50, 50, 49, 50, 50] 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, 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/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542656383 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 Building ZINC000542656383 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000542656383 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 935) grep: /scratch/xiaobo/83235/xao-8058115.15/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]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656383.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542656383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656383 none C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 18, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 44, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 44, 44, 50, 50, 50, 50, 50] 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, 45]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 936) grep: /scratch/xiaobo/83235/xao-8058115.15/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]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656383.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542656383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656383 none C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 18, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 44, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 44, 44, 50, 50, 50, 50, 50] 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, 45]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 937) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/937: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656383.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000542656383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656383 none C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 18, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 42, 50, 50, 49, 50, 50, 25, 25, 25, 25, 25, 3, 3, 3, 3, 3, 25, 25, 42, 42, 50, 50, 49, 50, 50] 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, 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/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 938) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/938: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656383.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000542656383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656383 none C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 18, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 42, 50, 50, 49, 50, 50, 25, 25, 25, 25, 25, 3, 3, 3, 3, 3, 25, 25, 42, 42, 50, 50, 49, 50, 50] 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, 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/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542656383 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 Building ZINC000542656383 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000542656383 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 935) grep: /scratch/xiaobo/83235/xao-8058115.15/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]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656383.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542656383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656383 none C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 18, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 44, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 44, 44, 50, 50, 50, 50, 50] 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, 45]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 936) grep: /scratch/xiaobo/83235/xao-8058115.15/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]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656383.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542656383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656383 none C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 18, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 44, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 44, 44, 50, 50, 50, 50, 50] 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, 45]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 937) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/937: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656383.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000542656383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656383 none C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 18, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 42, 50, 50, 49, 50, 50, 25, 25, 25, 25, 25, 3, 3, 3, 3, 3, 25, 25, 42, 42, 50, 50, 49, 50, 50] 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, 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/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 938) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/938: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656383.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000542656383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656383 none C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 18, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 42, 50, 50, 49, 50, 50, 25, 25, 25, 25, 25, 3, 3, 3, 3, 3, 25, 25, 42, 42, 50, 50, 49, 50, 50] 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, 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/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542656383 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 Building ZINC000542656383 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000542656383 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 935) grep: /scratch/xiaobo/83235/xao-8058115.15/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]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656383.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542656383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656383 none C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 18, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 44, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 44, 44, 50, 50, 50, 50, 50] 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, 45]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 936) grep: /scratch/xiaobo/83235/xao-8058115.15/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]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656383.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542656383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656383 none C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 18, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 44, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 44, 44, 50, 50, 50, 50, 50] 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, 45]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 937) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/937: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656383.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000542656383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656383 none C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 18, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 42, 50, 50, 49, 50, 50, 25, 25, 25, 25, 25, 3, 3, 3, 3, 3, 25, 25, 42, 42, 50, 50, 49, 50, 50] 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, 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/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 938) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/938: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1) `ZINC000542656383.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000542656383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000542656383 none C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.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', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 18, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 42, 50, 50, 49, 50, 50, 25, 25, 25, 25, 25, 3, 3, 3, 3, 3, 25, 25, 42, 42, 50, 50, 49, 50, 50] 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, 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/83235/xao-8058115.15/working/building/ZINC000542656383 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542656383 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656383 Building ZINC000542656943 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000542656943 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/939 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2c(F)cccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542656943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656943 none O=C(N[C@@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 26, 26, 26, 26, 26, 49, 49, 49, 48, 49, 49, 49, 26, 1, 1, 1, 5, 5, 1, 1, 5, 5, 4, 26, 26, 26, 26, 49, 48, 49, 26, 26, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/940 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/940' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2c(F)cccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542656943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656943 none O=C(N[C@@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 26, 26, 26, 26, 26, 49, 49, 49, 48, 49, 49, 49, 26, 1, 1, 1, 5, 5, 1, 1, 5, 5, 4, 26, 26, 26, 26, 49, 48, 49, 26, 26, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/941 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/941' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2c(F)cccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656943.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000542656943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656943 none O=C(N[C@@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 10, 28, 28, 28, 28, 28, 48, 48, 48, 48, 48, 48, 48, 28, 1, 1, 1, 5, 5, 1, 1, 5, 5, 5, 28, 28, 28, 28, 48, 48, 48, 28, 28, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/942 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/942' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2c(F)cccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656943.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000542656943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656943 none O=C(N[C@@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 10, 28, 28, 28, 28, 28, 48, 48, 48, 48, 48, 48, 48, 28, 1, 1, 1, 5, 5, 1, 1, 5, 5, 5, 28, 28, 28, 28, 48, 48, 48, 28, 28, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542656943 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 Building ZINC000542656943 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000542656943 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 939) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@@H]1CCN(c2c(F)cccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542656943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656943 none O=C(N[C@@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 26, 26, 26, 26, 26, 49, 49, 49, 48, 49, 49, 49, 26, 1, 1, 1, 5, 5, 1, 1, 5, 5, 4, 26, 26, 26, 26, 49, 48, 49, 26, 26, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 940) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@@H]1CCN(c2c(F)cccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542656943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656943 none O=C(N[C@@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 26, 26, 26, 26, 26, 49, 49, 49, 48, 49, 49, 49, 26, 1, 1, 1, 5, 5, 1, 1, 5, 5, 4, 26, 26, 26, 26, 49, 48, 49, 26, 26, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 941) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/941: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(c2c(F)cccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656943.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000542656943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656943 none O=C(N[C@@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 10, 28, 28, 28, 28, 28, 48, 48, 48, 48, 48, 48, 48, 28, 1, 1, 1, 5, 5, 1, 1, 5, 5, 5, 28, 28, 28, 28, 48, 48, 48, 28, 28, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 942) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/942: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(c2c(F)cccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656943.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000542656943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656943 none O=C(N[C@@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 10, 28, 28, 28, 28, 28, 48, 48, 48, 48, 48, 48, 48, 28, 1, 1, 1, 5, 5, 1, 1, 5, 5, 5, 28, 28, 28, 28, 48, 48, 48, 28, 28, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542656943 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 Building ZINC000542656943 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000542656943 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 939) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@@H]1CCN(c2c(F)cccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542656943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656943 none O=C(N[C@@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 26, 26, 26, 26, 26, 49, 49, 49, 48, 49, 49, 49, 26, 1, 1, 1, 5, 5, 1, 1, 5, 5, 4, 26, 26, 26, 26, 49, 48, 49, 26, 26, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 940) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@@H]1CCN(c2c(F)cccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542656943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656943 none O=C(N[C@@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 26, 26, 26, 26, 26, 49, 49, 49, 48, 49, 49, 49, 26, 1, 1, 1, 5, 5, 1, 1, 5, 5, 4, 26, 26, 26, 26, 49, 48, 49, 26, 26, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 941) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/941: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(c2c(F)cccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656943.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000542656943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656943 none O=C(N[C@@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 10, 28, 28, 28, 28, 28, 48, 48, 48, 48, 48, 48, 48, 28, 1, 1, 1, 5, 5, 1, 1, 5, 5, 5, 28, 28, 28, 28, 48, 48, 48, 28, 28, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 942) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/942: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(c2c(F)cccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656943.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000542656943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656943 none O=C(N[C@@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 10, 28, 28, 28, 28, 28, 48, 48, 48, 48, 48, 48, 48, 28, 1, 1, 1, 5, 5, 1, 1, 5, 5, 5, 28, 28, 28, 28, 48, 48, 48, 28, 28, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542656943 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 Building ZINC000542656943 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000542656943 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 939) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@@H]1CCN(c2c(F)cccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542656943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656943 none O=C(N[C@@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 26, 26, 26, 26, 26, 49, 49, 49, 48, 49, 49, 49, 26, 1, 1, 1, 5, 5, 1, 1, 5, 5, 4, 26, 26, 26, 26, 49, 48, 49, 26, 26, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 940) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@@H]1CCN(c2c(F)cccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542656943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656943 none O=C(N[C@@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 26, 26, 26, 26, 26, 49, 49, 49, 48, 49, 49, 49, 26, 1, 1, 1, 5, 5, 1, 1, 5, 5, 4, 26, 26, 26, 26, 49, 48, 49, 26, 26, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 941) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/941: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(c2c(F)cccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656943.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000542656943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656943 none O=C(N[C@@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 10, 28, 28, 28, 28, 28, 48, 48, 48, 48, 48, 48, 48, 28, 1, 1, 1, 5, 5, 1, 1, 5, 5, 5, 28, 28, 28, 28, 48, 48, 48, 28, 28, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 942) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/942: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(c2c(F)cccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656943.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000542656943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656943 none O=C(N[C@@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 10, 28, 28, 28, 28, 28, 48, 48, 48, 48, 48, 48, 48, 28, 1, 1, 1, 5, 5, 1, 1, 5, 5, 5, 28, 28, 28, 28, 48, 48, 48, 28, 28, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542656943 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656943 Building ZINC000542656944 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000542656944 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/943 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2c(F)cccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656944.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542656944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656944 none O=C(N[C@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 10, 28, 28, 28, 28, 28, 47, 47, 47, 46, 47, 47, 47, 28, 1, 1, 1, 5, 5, 1, 2, 5, 5, 5, 28, 28, 28, 28, 47, 47, 47, 28, 28, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/944 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/944' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2c(F)cccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656944.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542656944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656944 none O=C(N[C@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 10, 28, 28, 28, 28, 28, 47, 47, 47, 46, 47, 47, 47, 28, 1, 1, 1, 5, 5, 1, 2, 5, 5, 5, 28, 28, 28, 28, 47, 47, 47, 28, 28, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/945 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/945' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2c(F)cccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656944.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000542656944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656944 none O=C(N[C@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 25, 25, 25, 25, 25, 47, 47, 47, 25, 47, 47, 47, 25, 1, 1, 1, 5, 5, 1, 1, 5, 5, 4, 25, 25, 25, 25, 47, 25, 47, 25, 25, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/946 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/946' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2c(F)cccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656944.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000542656944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656944 none O=C(N[C@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 25, 25, 25, 25, 25, 47, 47, 47, 25, 47, 47, 47, 25, 1, 1, 1, 5, 5, 1, 1, 5, 5, 4, 25, 25, 25, 25, 47, 25, 47, 25, 25, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542656944 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 Building ZINC000542656944 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000542656944 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 943) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H]1CCN(c2c(F)cccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656944.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542656944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656944 none O=C(N[C@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 10, 28, 28, 28, 28, 28, 47, 47, 47, 46, 47, 47, 47, 28, 1, 1, 1, 5, 5, 1, 2, 5, 5, 5, 28, 28, 28, 28, 47, 47, 47, 28, 28, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 944) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H]1CCN(c2c(F)cccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656944.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542656944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656944 none O=C(N[C@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 10, 28, 28, 28, 28, 28, 47, 47, 47, 46, 47, 47, 47, 28, 1, 1, 1, 5, 5, 1, 2, 5, 5, 5, 28, 28, 28, 28, 47, 47, 47, 28, 28, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 945) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/945: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(c2c(F)cccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656944.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000542656944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656944 none O=C(N[C@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 25, 25, 25, 25, 25, 47, 47, 47, 25, 47, 47, 47, 25, 1, 1, 1, 5, 5, 1, 1, 5, 5, 4, 25, 25, 25, 25, 47, 25, 47, 25, 25, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 946) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/946: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(c2c(F)cccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656944.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000542656944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656944 none O=C(N[C@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 25, 25, 25, 25, 25, 47, 47, 47, 25, 47, 47, 47, 25, 1, 1, 1, 5, 5, 1, 1, 5, 5, 4, 25, 25, 25, 25, 47, 25, 47, 25, 25, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542656944 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 Building ZINC000542656944 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000542656944 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 943) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H]1CCN(c2c(F)cccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656944.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542656944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656944 none O=C(N[C@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 10, 28, 28, 28, 28, 28, 47, 47, 47, 46, 47, 47, 47, 28, 1, 1, 1, 5, 5, 1, 2, 5, 5, 5, 28, 28, 28, 28, 47, 47, 47, 28, 28, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 944) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H]1CCN(c2c(F)cccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656944.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542656944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656944 none O=C(N[C@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 10, 28, 28, 28, 28, 28, 47, 47, 47, 46, 47, 47, 47, 28, 1, 1, 1, 5, 5, 1, 2, 5, 5, 5, 28, 28, 28, 28, 47, 47, 47, 28, 28, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 945) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/945: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(c2c(F)cccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656944.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000542656944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656944 none O=C(N[C@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 25, 25, 25, 25, 25, 47, 47, 47, 25, 47, 47, 47, 25, 1, 1, 1, 5, 5, 1, 1, 5, 5, 4, 25, 25, 25, 25, 47, 25, 47, 25, 25, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 946) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/946: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(c2c(F)cccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656944.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000542656944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656944 none O=C(N[C@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 25, 25, 25, 25, 25, 47, 47, 47, 25, 47, 47, 47, 25, 1, 1, 1, 5, 5, 1, 1, 5, 5, 4, 25, 25, 25, 25, 47, 25, 47, 25, 25, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542656944 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 Building ZINC000542656944 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000542656944 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 943) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H]1CCN(c2c(F)cccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656944.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542656944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656944 none O=C(N[C@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 10, 28, 28, 28, 28, 28, 47, 47, 47, 46, 47, 47, 47, 28, 1, 1, 1, 5, 5, 1, 2, 5, 5, 5, 28, 28, 28, 28, 47, 47, 47, 28, 28, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 944) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@H]1CCN(c2c(F)cccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656944.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542656944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656944 none O=C(N[C@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 10, 28, 28, 28, 28, 28, 47, 47, 47, 46, 47, 47, 47, 28, 1, 1, 1, 5, 5, 1, 2, 5, 5, 5, 28, 28, 28, 28, 47, 47, 47, 28, 28, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 945) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/945: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(c2c(F)cccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656944.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000542656944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656944 none O=C(N[C@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 25, 25, 25, 25, 25, 47, 47, 47, 25, 47, 47, 47, 25, 1, 1, 1, 5, 5, 1, 1, 5, 5, 4, 25, 25, 25, 25, 47, 25, 47, 25, 25, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 946) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/946: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(c2c(F)cccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000542656944.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000542656944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000542656944 none O=C(N[C@H]1CCN(c2c(F)cccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 25, 25, 25, 25, 25, 47, 47, 47, 25, 47, 47, 47, 25, 1, 1, 1, 5, 5, 1, 1, 5, 5, 4, 25, 25, 25, 25, 47, 25, 47, 25, 25, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542656944 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542656944 Building ZINC000542858826 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542858826' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542858826 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542858826 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542858826/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542858826 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/947 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1nc(O)c2ccccc2n1) `ZINC000542858826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542858826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542858826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000542858826 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1nc(O)c2ccccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 12, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 10, 27, 27, 27, 27, 21, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 10, 54, 27, 27, 27, 27] 74 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 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: 124 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542858826 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542858826/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542858826 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/948 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/948' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1nc(O)c2ccccc2n1) `ZINC000542858826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542858826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542858826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000542858826 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1nc(O)c2ccccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 12, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 10, 17, 27, 27, 27, 21, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 10, 54, 27, 27, 27, 27] 74 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 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: 126 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542858826 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542858826 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542858826/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542858826/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542858826 Building ZINC000542858826 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542858826' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542858826 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542858826 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542858826/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542858826 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 947) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1nc(O)c2ccccc2n1) `ZINC000542858826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542858826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542858826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000542858826 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1nc(O)c2ccccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 12, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 10, 27, 27, 27, 27, 21, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 10, 54, 27, 27, 27, 27] 74 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 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: 124 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542858826 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542858826/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542858826 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 948) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1nc(O)c2ccccc2n1) `ZINC000542858826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542858826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542858826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000542858826 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1nc(O)c2ccccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 12, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 10, 17, 27, 27, 27, 21, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 10, 54, 27, 27, 27, 27] 74 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 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: 126 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542858826 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000542858826 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542858826/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542858826/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000542858826 Building ZINC000111415797 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415797' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415797 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000111415797 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415797/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415797 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/949 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3)OC[C@H]2C)cc1) `ZINC000111415797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000111415797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111415797 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3)OC[C@H]2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 1, 10, 10, 1, 1, 1, 1, 8, 13, 18, 18, 18, 18, 40, 40, 21, 40, 40, 18, 18, 18, 18, 18, 10, 10, 10, 10, 10, 10, 10, 18, 18, 40, 40, 40, 40, 40, 18, 18, 18, 18, 18, 10, 10] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 171 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415797 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415797/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415797 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/950 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/950' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3)OC[C@H]2C)cc1) `ZINC000111415797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000111415797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111415797 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3)OC[C@H]2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 1, 11, 11, 1, 1, 1, 1, 9, 13, 18, 18, 18, 18, 40, 40, 23, 40, 40, 18, 18, 18, 18, 18, 11, 11, 11, 11, 11, 11, 11, 18, 18, 40, 40, 40, 40, 40, 18, 18, 18, 18, 18, 11, 11] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 167 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415797 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000111415797 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415797/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415797/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415797 Building ZINC000111415797 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415797' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415797 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000111415797 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415797/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415797 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 949) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3)OC[C@H]2C)cc1) `ZINC000111415797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000111415797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111415797 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3)OC[C@H]2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 1, 10, 10, 1, 1, 1, 1, 8, 13, 18, 18, 18, 18, 40, 40, 21, 40, 40, 18, 18, 18, 18, 18, 10, 10, 10, 10, 10, 10, 10, 18, 18, 40, 40, 40, 40, 40, 18, 18, 18, 18, 18, 10, 10] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 171 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415797 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415797/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415797 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 950) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3)OC[C@H]2C)cc1) `ZINC000111415797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000111415797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111415797 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3)OC[C@H]2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 1, 11, 11, 1, 1, 1, 1, 9, 13, 18, 18, 18, 18, 40, 40, 23, 40, 40, 18, 18, 18, 18, 18, 11, 11, 11, 11, 11, 11, 11, 18, 18, 40, 40, 40, 40, 40, 18, 18, 18, 18, 18, 11, 11] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 167 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415797 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000111415797 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415797/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415797/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415797 Building ZINC000111415799 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415799' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415799 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000111415799 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415799/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415799 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/951 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3)OC[C@@H]2C)cc1) `ZINC000111415799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000111415799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111415799 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3)OC[C@@H]2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 7, 7, 1, 1, 1, 2, 14, 16, 20, 20, 20, 20, 42, 42, 25, 42, 42, 20, 20, 20, 20, 20, 7, 7, 7, 7, 7, 7, 7, 20, 20, 42, 42, 25, 42, 42, 20, 20, 20, 20, 20, 7, 7] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415799 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415799/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415799 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/952 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/952' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3)OC[C@@H]2C)cc1) `ZINC000111415799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000111415799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111415799 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3)OC[C@@H]2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 5, 1, 1, 1, 2, 16, 19, 27, 27, 27, 27, 48, 48, 33, 48, 48, 27, 27, 27, 27, 27, 5, 5, 5, 5, 5, 5, 5, 27, 27, 48, 48, 33, 48, 48, 27, 27, 27, 27, 27, 5, 5] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 141 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415799 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000111415799 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415799/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415799/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415799 Building ZINC000111415799 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415799' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415799 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000111415799 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415799/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415799 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 951) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3)OC[C@@H]2C)cc1) `ZINC000111415799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000111415799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111415799 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3)OC[C@@H]2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 7, 7, 1, 1, 1, 2, 14, 16, 20, 20, 20, 20, 42, 42, 25, 42, 42, 20, 20, 20, 20, 20, 7, 7, 7, 7, 7, 7, 7, 20, 20, 42, 42, 25, 42, 42, 20, 20, 20, 20, 20, 7, 7] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415799 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415799/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415799 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 952) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3)OC[C@@H]2C)cc1) `ZINC000111415799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000111415799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111415799 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3)OC[C@@H]2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 5, 1, 1, 1, 2, 16, 19, 27, 27, 27, 27, 48, 48, 33, 48, 48, 27, 27, 27, 27, 27, 5, 5, 5, 5, 5, 5, 5, 27, 27, 48, 48, 33, 48, 48, 27, 27, 27, 27, 27, 5, 5] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 141 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415799 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000111415799 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415799/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415799/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415799 Building ZINC000111415802 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415802' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415802 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000111415802 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415802/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415802 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/953 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](c3ccccc3)OC[C@H]2C)cc1) `ZINC000111415802.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000111415802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111415802 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](c3ccccc3)OC[C@H]2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 1, 7, 7, 1, 1, 1, 5, 15, 18, 24, 24, 24, 24, 47, 47, 24, 47, 47, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 7, 24, 24, 47, 47, 24, 47, 47, 24, 24, 24, 24, 24, 7, 7] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 160 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415802 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415802/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415802 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/954 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/954' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](c3ccccc3)OC[C@H]2C)cc1) `ZINC000111415802.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000111415802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415802/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111415802 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](c3ccccc3)OC[C@H]2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 7, 7, 1, 1, 1, 4, 15, 17, 20, 20, 20, 20, 42, 42, 20, 42, 42, 20, 20, 20, 20, 20, 7, 7, 7, 7, 7, 7, 7, 20, 20, 42, 42, 20, 42, 42, 20, 20, 20, 20, 20, 7, 7] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415802 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000111415802 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415802/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415802/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415802 Building ZINC000111415802 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415802' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415802 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000111415802 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415802/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415802 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 953) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](c3ccccc3)OC[C@H]2C)cc1) `ZINC000111415802.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000111415802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111415802 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](c3ccccc3)OC[C@H]2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 1, 7, 7, 1, 1, 1, 5, 15, 18, 24, 24, 24, 24, 47, 47, 24, 47, 47, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 7, 24, 24, 47, 47, 24, 47, 47, 24, 24, 24, 24, 24, 7, 7] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 160 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415802 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415802/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415802 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 954) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](c3ccccc3)OC[C@H]2C)cc1) `ZINC000111415802.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000111415802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415802/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111415802 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](c3ccccc3)OC[C@H]2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 7, 7, 1, 1, 1, 4, 15, 17, 20, 20, 20, 20, 42, 42, 20, 42, 42, 20, 20, 20, 20, 20, 7, 7, 7, 7, 7, 7, 7, 20, 20, 42, 42, 20, 42, 42, 20, 20, 20, 20, 20, 7, 7] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415802 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000111415802 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415802/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415802/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415802 Building ZINC000111415804 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415804' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415804 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000111415804 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415804/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415804 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/955 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](c3ccccc3)OC[C@@H]2C)cc1) `ZINC000111415804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000111415804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111415804 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](c3ccccc3)OC[C@@H]2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 1, 11, 11, 1, 1, 1, 1, 7, 11, 16, 16, 16, 16, 39, 39, 16, 39, 39, 16, 16, 16, 16, 16, 11, 11, 11, 11, 11, 11, 11, 16, 16, 39, 39, 16, 39, 39, 16, 16, 16, 16, 16, 11, 11] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 152 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415804 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415804/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415804 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/956 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/956' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](c3ccccc3)OC[C@@H]2C)cc1) `ZINC000111415804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000111415804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111415804 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](c3ccccc3)OC[C@@H]2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 9, 9, 1, 1, 1, 1, 8, 12, 17, 17, 17, 17, 41, 41, 17, 41, 41, 17, 17, 17, 17, 17, 9, 9, 9, 9, 9, 9, 9, 17, 17, 41, 41, 17, 41, 41, 17, 17, 17, 17, 17, 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, 45]) total number of confs: 154 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415804 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000111415804 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415804/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415804/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415804 Building ZINC000111415804 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415804' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415804 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000111415804 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415804/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415804 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 955) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](c3ccccc3)OC[C@@H]2C)cc1) `ZINC000111415804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000111415804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111415804 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](c3ccccc3)OC[C@@H]2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 1, 11, 11, 1, 1, 1, 1, 7, 11, 16, 16, 16, 16, 39, 39, 16, 39, 39, 16, 16, 16, 16, 16, 11, 11, 11, 11, 11, 11, 11, 16, 16, 39, 39, 16, 39, 39, 16, 16, 16, 16, 16, 11, 11] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 152 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415804 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415804/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415804 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 956) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](c3ccccc3)OC[C@@H]2C)cc1) `ZINC000111415804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000111415804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111415804 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](c3ccccc3)OC[C@@H]2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 9, 9, 1, 1, 1, 1, 8, 12, 17, 17, 17, 17, 41, 41, 17, 41, 41, 17, 17, 17, 17, 17, 9, 9, 9, 9, 9, 9, 9, 17, 17, 41, 41, 17, 41, 41, 17, 17, 17, 17, 17, 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, 45]) total number of confs: 154 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415804 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000111415804 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415804/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415804/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111415804 Building ZINC000111418979 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000111418979 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/957 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000111418979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418979 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 15, 15, 15, 26, 26, 33, 48, 48, 36, 48, 48, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 15, 15, 15, 26, 26, 26, 33, 33, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/958 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/958' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000111418979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418979 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 24, 24, 31, 46, 46, 34, 46, 46, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 14, 14, 14, 24, 24, 24, 31, 31, 46, 46, 46, 46, 46, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/959 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/959' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418979.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000111418979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418979 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 15, 15, 15, 26, 26, 33, 48, 48, 36, 48, 48, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 15, 15, 15, 26, 26, 26, 33, 33, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/960 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/960' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418979.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000111418979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418979 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 24, 24, 31, 46, 46, 34, 46, 46, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 14, 14, 14, 24, 24, 24, 31, 31, 46, 46, 46, 46, 46, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000111418979 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 Building ZINC000111418979 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000111418979 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 957) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000111418979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418979 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 15, 15, 15, 26, 26, 33, 48, 48, 36, 48, 48, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 15, 15, 15, 26, 26, 26, 33, 33, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 958) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000111418979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418979 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 24, 24, 31, 46, 46, 34, 46, 46, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 14, 14, 14, 24, 24, 24, 31, 31, 46, 46, 46, 46, 46, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 959) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418979.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000111418979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418979 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 15, 15, 15, 26, 26, 33, 48, 48, 36, 48, 48, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 15, 15, 15, 26, 26, 26, 33, 33, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 960) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/960: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418979.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000111418979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418979 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 24, 24, 31, 46, 46, 34, 46, 46, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 14, 14, 14, 24, 24, 24, 31, 31, 46, 46, 46, 46, 46, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000111418979 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 Building ZINC000111418979 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000111418979 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 957) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000111418979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418979 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 15, 15, 15, 26, 26, 33, 48, 48, 36, 48, 48, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 15, 15, 15, 26, 26, 26, 33, 33, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 958) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000111418979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418979 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 24, 24, 31, 46, 46, 34, 46, 46, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 14, 14, 14, 24, 24, 24, 31, 31, 46, 46, 46, 46, 46, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 959) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418979.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000111418979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418979 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 15, 15, 15, 26, 26, 33, 48, 48, 36, 48, 48, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 15, 15, 15, 26, 26, 26, 33, 33, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 960) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/960: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418979.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000111418979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418979 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 24, 24, 31, 46, 46, 34, 46, 46, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 14, 14, 14, 24, 24, 24, 31, 31, 46, 46, 46, 46, 46, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000111418979 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 Building ZINC000111418979 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000111418979 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 957) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000111418979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418979 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 15, 15, 15, 26, 26, 33, 48, 48, 36, 48, 48, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 15, 15, 15, 26, 26, 26, 33, 33, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 958) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000111418979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418979 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 24, 24, 31, 46, 46, 34, 46, 46, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 14, 14, 14, 24, 24, 24, 31, 31, 46, 46, 46, 46, 46, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 959) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418979.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000111418979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418979 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 15, 15, 15, 26, 26, 33, 48, 48, 36, 48, 48, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 15, 15, 15, 26, 26, 26, 33, 33, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 960) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/960: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418979.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000111418979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418979 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 24, 24, 31, 46, 46, 34, 46, 46, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 14, 14, 14, 24, 24, 24, 31, 31, 46, 46, 46, 46, 46, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000111418979 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418979 Building ZINC000111418981 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000111418981 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/961 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000111418981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418981 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 13, 13, 13, 23, 23, 30, 46, 46, 40, 46, 46, 4, 4, 4, 4, 4, 4, 4, 2, 8, 8, 13, 13, 13, 23, 23, 23, 30, 30, 46, 46, 46, 46, 46, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/962 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/962' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000111418981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418981 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 25, 25, 32, 48, 48, 44, 48, 48, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 14, 14, 14, 25, 25, 25, 32, 32, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/963 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/963' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418981.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000111418981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418981 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 13, 13, 13, 23, 23, 30, 46, 46, 40, 46, 46, 4, 4, 4, 4, 4, 4, 4, 2, 8, 8, 13, 13, 13, 23, 23, 23, 30, 30, 46, 46, 46, 46, 46, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/964 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/964' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418981.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000111418981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418981 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 25, 25, 32, 48, 48, 44, 48, 48, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 14, 14, 14, 25, 25, 25, 32, 32, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000111418981 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 Building ZINC000111418981 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000111418981 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 961) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000111418981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418981 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 13, 13, 13, 23, 23, 30, 46, 46, 40, 46, 46, 4, 4, 4, 4, 4, 4, 4, 2, 8, 8, 13, 13, 13, 23, 23, 23, 30, 30, 46, 46, 46, 46, 46, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 962) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000111418981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418981 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 25, 25, 32, 48, 48, 44, 48, 48, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 14, 14, 14, 25, 25, 25, 32, 32, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 963) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/963: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418981.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000111418981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418981 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 13, 13, 13, 23, 23, 30, 46, 46, 40, 46, 46, 4, 4, 4, 4, 4, 4, 4, 2, 8, 8, 13, 13, 13, 23, 23, 23, 30, 30, 46, 46, 46, 46, 46, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 964) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/964: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418981.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000111418981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418981 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 25, 25, 32, 48, 48, 44, 48, 48, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 14, 14, 14, 25, 25, 25, 32, 32, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000111418981 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 Building ZINC000111418981 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000111418981 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 961) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000111418981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418981 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 13, 13, 13, 23, 23, 30, 46, 46, 40, 46, 46, 4, 4, 4, 4, 4, 4, 4, 2, 8, 8, 13, 13, 13, 23, 23, 23, 30, 30, 46, 46, 46, 46, 46, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 962) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000111418981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418981 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 25, 25, 32, 48, 48, 44, 48, 48, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 14, 14, 14, 25, 25, 25, 32, 32, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 963) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/963: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418981.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000111418981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418981 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 13, 13, 13, 23, 23, 30, 46, 46, 40, 46, 46, 4, 4, 4, 4, 4, 4, 4, 2, 8, 8, 13, 13, 13, 23, 23, 23, 30, 30, 46, 46, 46, 46, 46, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 964) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/964: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418981.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000111418981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418981 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 25, 25, 32, 48, 48, 44, 48, 48, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 14, 14, 14, 25, 25, 25, 32, 32, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000111418981 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 Building ZINC000111418981 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000111418981 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 961) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000111418981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418981 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 13, 13, 13, 23, 23, 30, 46, 46, 40, 46, 46, 4, 4, 4, 4, 4, 4, 4, 2, 8, 8, 13, 13, 13, 23, 23, 23, 30, 30, 46, 46, 46, 46, 46, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 962) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000111418981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418981 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 25, 25, 32, 48, 48, 44, 48, 48, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 14, 14, 14, 25, 25, 25, 32, 32, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `2' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/2 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 2 (index: 963) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/963: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418981.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000111418981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418981 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 13, 13, 13, 23, 23, 30, 46, 46, 40, 46, 46, 4, 4, 4, 4, 4, 4, 4, 2, 8, 8, 13, 13, 13, 23, 23, 23, 30, 30, 46, 46, 46, 46, 46, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `3' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/3 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 3 (index: 964) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/964: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1) `ZINC000111418981.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000111418981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111418981 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)N(C)Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 25, 25, 32, 48, 48, 44, 48, 48, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 14, 14, 14, 25, 25, 25, 32, 32, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000111418981 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 2: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/2.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/0.* 3: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981/3.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111418981 Building ZINC000057571561 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000057571561' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000057571561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000057571561 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000057571561/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000057571561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/965 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/965' -> `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)Nc1ccnn1C1CCCCC1) `ZINC000057571561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000057571561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000057571561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000057571561 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccnn1C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 15, 15, 15, 15, 22, 42, 42, 42, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 15, 15, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000057571561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000057571561/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000057571561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/966 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/966' -> `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)Nc1ccnn1C1CCCCC1) `ZINC000057571561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000057571561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000057571561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000057571561 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccnn1C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 8, 17, 17, 17, 17, 24, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 17, 17, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 123 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000057571561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000057571561 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000057571561/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000057571561/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000057571561 Building ZINC000057571561 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000057571561' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000057571561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000057571561 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000057571561/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000057571561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 965) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccnn1C1CCCCC1) `ZINC000057571561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000057571561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000057571561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000057571561 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccnn1C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 15, 15, 15, 15, 22, 42, 42, 42, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 15, 15, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000057571561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000057571561/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000057571561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 966) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccnn1C1CCCCC1) `ZINC000057571561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000057571561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000057571561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000057571561 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccnn1C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 8, 17, 17, 17, 17, 24, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 17, 17, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 123 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000057571561 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000057571561 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000057571561/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000057571561/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000057571561 Building ZINC000911548023 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000911548023' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000911548023 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000911548023 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000911548023/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000911548023 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/967 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(C)(C(=O)OC(C)(C)C)CC1) `ZINC000911548023.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000911548023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000911548023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000911548023 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(C)(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 16, 16, 17, 17, 17, 17, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000911548023 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000911548023/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000911548023 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/968 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/968' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(C)(C(=O)OC(C)(C)C)CC1) `ZINC000911548023.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000911548023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000911548023/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000911548023 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(C)(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 4, 6, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7, 7] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000911548023 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000911548023 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000911548023/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000911548023/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000911548023 Building ZINC000911548023 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000911548023' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000911548023 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000911548023 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000911548023/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000911548023 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 967) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(C)(C(=O)OC(C)(C)C)CC1) `ZINC000911548023.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000911548023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000911548023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000911548023 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(C)(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 16, 16, 17, 17, 17, 17, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000911548023 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000911548023/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000911548023 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 968) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(C)(C(=O)OC(C)(C)C)CC1) `ZINC000911548023.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000911548023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000911548023/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000911548023 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(C)(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 4, 6, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7, 7] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000911548023 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000911548023 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000911548023/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000911548023/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000911548023 Building ZINC000762678999 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762678999' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762678999 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000762678999 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762678999/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762678999 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/969 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@H]2SCCS[C@H]12)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000762678999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000762678999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762678999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000762678999 none O=C(N[C@@H]1CC[C@H]2SCCS[C@H]12)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 14, 5, 5, 14, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 7, 28, 28, 28, 28, 28, 28, 28, 28, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762678999 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762678999/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762678999 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/970 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/970' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@H]2SCCS[C@H]12)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000762678999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000762678999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762678999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000762678999 none O=C(N[C@@H]1CC[C@H]2SCCS[C@H]12)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 14, 5, 5, 14, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 6, 20, 20, 20, 20, 20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762678999 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000762678999 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762678999/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762678999/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762678999 Building ZINC000762678999 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762678999' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762678999 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000762678999 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762678999/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762678999 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 969) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@@H]1CC[C@H]2SCCS[C@H]12)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000762678999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000762678999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762678999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000762678999 none O=C(N[C@@H]1CC[C@H]2SCCS[C@H]12)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 14, 5, 5, 14, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 7, 28, 28, 28, 28, 28, 28, 28, 28, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762678999 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762678999/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762678999 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 970) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@@H]1CC[C@H]2SCCS[C@H]12)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000762678999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000762678999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762678999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000762678999 none O=C(N[C@@H]1CC[C@H]2SCCS[C@H]12)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 14, 5, 5, 14, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 6, 20, 20, 20, 20, 20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762678999 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000762678999 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762678999/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762678999/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762678999 Building ZINC000762679001 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679001' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679001 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000762679001 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679001/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679001 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/971 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@@H]2SCCS[C@H]12)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000762679001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000762679001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000762679001 none O=C(N[C@@H]1CC[C@@H]2SCCS[C@H]12)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 14, 5, 5, 14, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 72 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679001 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679001/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679001 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/972 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/972' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@@H]2SCCS[C@H]12)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000762679001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000762679001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000762679001 none O=C(N[C@@H]1CC[C@@H]2SCCS[C@H]12)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 14, 5, 5, 14, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 66 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679001 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000762679001 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679001/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679001/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679001 Building ZINC000762679001 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679001' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679001 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000762679001 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679001/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679001 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 971) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@@H]1CC[C@@H]2SCCS[C@H]12)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000762679001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000762679001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000762679001 none O=C(N[C@@H]1CC[C@@H]2SCCS[C@H]12)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 14, 5, 5, 14, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 72 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679001 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679001/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679001 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 972) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@@H]1CC[C@@H]2SCCS[C@H]12)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000762679001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000762679001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000762679001 none O=C(N[C@@H]1CC[C@@H]2SCCS[C@H]12)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 14, 5, 5, 14, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 66 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679001 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000762679001 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679001/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679001/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679001 Building ZINC000762679003 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679003' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000762679003 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679003/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/973 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@H]2SCCS[C@@H]12)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000762679003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000762679003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000762679003 none O=C(N[C@@H]1CC[C@H]2SCCS[C@@H]12)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 14, 5, 5, 14, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679003/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/974 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/974' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@H]2SCCS[C@@H]12)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000762679003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000762679003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000762679003 none O=C(N[C@@H]1CC[C@H]2SCCS[C@@H]12)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 14, 5, 5, 14, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000762679003 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679003/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679003/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679003 Building ZINC000762679003 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679003' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000762679003 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679003/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 973) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@@H]1CC[C@H]2SCCS[C@@H]12)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000762679003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000762679003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000762679003 none O=C(N[C@@H]1CC[C@H]2SCCS[C@@H]12)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 14, 5, 5, 14, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679003/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 974) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@@H]1CC[C@H]2SCCS[C@@H]12)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000762679003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000762679003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000762679003 none O=C(N[C@@H]1CC[C@H]2SCCS[C@@H]12)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 14, 5, 5, 14, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679003 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000762679003 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679003/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679003/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679003 Building ZINC000762679007 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679007' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679007 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000762679007 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679007/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679007 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/975 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@@H]2SCCS[C@@H]12)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000762679007.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000762679007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000762679007 none O=C(N[C@@H]1CC[C@@H]2SCCS[C@@H]12)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 14, 5, 5, 14, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 11, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 6, 30, 30, 30, 30, 30, 30, 30, 30, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679007 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679007/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679007 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/976 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/976' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@@H]2SCCS[C@@H]12)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000762679007.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000762679007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000762679007 none O=C(N[C@@H]1CC[C@@H]2SCCS[C@@H]12)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 14, 5, 5, 14, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 6, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679007 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000762679007 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679007/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679007/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679007 Building ZINC000762679007 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679007' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679007 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000762679007 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679007/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679007 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 975) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@@H]1CC[C@@H]2SCCS[C@@H]12)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000762679007.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000762679007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000762679007 none O=C(N[C@@H]1CC[C@@H]2SCCS[C@@H]12)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 14, 5, 5, 14, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 11, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 6, 30, 30, 30, 30, 30, 30, 30, 30, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679007 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679007/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679007 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 976) grep: /scratch/xiaobo/83235/xao-8058115.15/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: O=C(N[C@@H]1CC[C@@H]2SCCS[C@@H]12)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000762679007.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000762679007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000762679007 none O=C(N[C@@H]1CC[C@@H]2SCCS[C@@H]12)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 14, 5, 5, 14, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 6, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679007 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000762679007 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679007/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679007/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000762679007 Building ZINC000444525901 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444525901' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444525901 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000444525901 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444525901/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444525901 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/977 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C)(C)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000444525901.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000444525901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444525901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000444525901 none CCOC(C)(C)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 16, 35, 33, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 47, 47, 47, 47, 47, 35, 35, 35, 35, 35, 35, 16, 16, 3, 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, 33, 34, 35, 36]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444525901 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444525901/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444525901 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/978 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/978' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C)(C)CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000444525901.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000444525901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444525901/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000444525901 none CCOC(C)(C)CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 16, 33, 35, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 47, 47, 47, 47, 47, 35, 35, 35, 35, 35, 35, 16, 16, 3, 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, 33, 34, 35, 36]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444525901 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000444525901 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444525901/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444525901/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444525901 Building ZINC000444525901 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444525901' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444525901 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000444525901 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444525901/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444525901 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 977) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCOC(C)(C)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000444525901.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000444525901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444525901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000444525901 none CCOC(C)(C)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 16, 35, 33, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 47, 47, 47, 47, 47, 35, 35, 35, 35, 35, 35, 16, 16, 3, 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, 33, 34, 35, 36]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444525901 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444525901/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444525901 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 978) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CCOC(C)(C)CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000444525901.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000444525901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444525901/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000444525901 none CCOC(C)(C)CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 16, 33, 35, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 47, 47, 47, 47, 47, 35, 35, 35, 35, 35, 35, 16, 16, 3, 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, 33, 34, 35, 36]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444525901 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000444525901 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444525901/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444525901/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000444525901 Building ZINC000111423348 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111423348' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111423348 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000111423348 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111423348/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111423348 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/979 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCCCN2CCCCC2)cc1) `ZINC000111423348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000111423348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111423348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000111423348 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCCCN2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 20, 26, 21, 31, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 2, 12, 12, 26, 26, 26, 26, 27, 27, 30, 31, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111423348 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111423348/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111423348 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/980 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/980' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCCCCN2CCCCC2)cc1) `ZINC000111423348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000111423348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111423348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000111423348 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCCCCN2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 20, 26, 21, 31, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 2, 12, 12, 26, 26, 26, 26, 27, 27, 31, 30, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111423348 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000111423348 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111423348/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111423348/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111423348 Building ZINC000111423348 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111423348' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111423348 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000111423348 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111423348/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111423348 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 979) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCCCN2CCCCC2)cc1) `ZINC000111423348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000111423348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111423348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000111423348 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCCCN2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 20, 26, 21, 31, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 2, 12, 12, 26, 26, 26, 26, 27, 27, 30, 31, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111423348 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111423348/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111423348 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 980) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)NCCCCCN2CCCCC2)cc1) `ZINC000111423348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000111423348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111423348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000111423348 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCCCCN2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 20, 26, 21, 31, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 2, 12, 12, 26, 26, 26, 26, 27, 27, 31, 30, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111423348 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000111423348 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111423348/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111423348/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000111423348 Building ZINC000174898786 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898786' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898786 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174898786 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898786/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898786 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/981 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000174898786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174898786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000174898786 none CC(C)(C)OC(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 7, 25, 7, 7, 7, 7, 2, 1, 4, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 2, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/83235/xao-8058115.15/working/building/ZINC000174898786 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898786/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898786 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/982 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/982' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000174898786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174898786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000174898786 none CC(C)(C)OC(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 4, 24, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898786 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174898786 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898786/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898786/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898786 Building ZINC000174898786 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898786' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898786 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174898786 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898786/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898786 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 981) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/981: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000174898786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174898786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000174898786 none CC(C)(C)OC(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 7, 25, 7, 7, 7, 7, 2, 1, 4, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 2, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/83235/xao-8058115.15/working/building/ZINC000174898786 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898786/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898786 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 982) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/982: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000174898786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174898786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000174898786 none CC(C)(C)OC(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 4, 24, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898786 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174898786 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898786/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898786/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898786 Building ZINC000174898805 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898805' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898805 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174898805 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898805/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898805 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/983 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000174898805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174898805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000174898805 none CC(C)(C)OC(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 28, 6, 28, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 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/83235/xao-8058115.15/working/building/ZINC000174898805 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898805/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898805 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/984 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/984' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000174898805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174898805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000174898805 none CC(C)(C)OC(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 5, 22, 5, 5, 5, 5, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898805 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174898805 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898805/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898805/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898805 Building ZINC000174898805 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898805' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898805 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174898805 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898805/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898805 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 983) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/983: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000174898805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174898805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000174898805 none CC(C)(C)OC(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 28, 6, 28, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 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/83235/xao-8058115.15/working/building/ZINC000174898805 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898805/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898805 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 984) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/984: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000174898805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174898805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000174898805 none CC(C)(C)OC(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 5, 22, 5, 5, 5, 5, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898805 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174898805 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898805/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898805/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174898805 Building ZINC000174908394 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908394' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174908394 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908394/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/985 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC000174908394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174908394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000174908394 none CC(C)(C)OC(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 10, 41, 10, 10, 10, 10, 2, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 2, 2, 2, 2, 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: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908394/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/986 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/986' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC000174908394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174908394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000174908394 none CC(C)(C)OC(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 8, 41, 8, 8, 8, 8, 2, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 2, 2, 2, 8, 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, 42]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174908394 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908394/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908394/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908394 Building ZINC000174908394 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908394' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174908394 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908394/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 985) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/985: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC000174908394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174908394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000174908394 none CC(C)(C)OC(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 10, 41, 10, 10, 10, 10, 2, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 2, 2, 2, 2, 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: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908394/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 986) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/986: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC000174908394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174908394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000174908394 none CC(C)(C)OC(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 8, 41, 8, 8, 8, 8, 2, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 2, 2, 2, 8, 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, 42]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908394 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174908394 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908394/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908394/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908394 Building ZINC000174908411 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908411' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908411 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174908411 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908411/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908411 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/987 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC000174908411.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174908411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000174908411 none CC(C)(C)OC(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 40, 9, 40, 9, 9, 9, 9, 2, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 2, 2, 2, 9, 9] 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: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908411 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908411/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908411 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/988 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/988' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC000174908411.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174908411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908411/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000174908411 none CC(C)(C)OC(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 40, 10, 40, 10, 10, 10, 10, 2, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 2, 2, 2, 2, 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: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908411 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174908411 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908411/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908411/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908411 Building ZINC000174908411 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908411' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908411 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174908411 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908411/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908411 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 987) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)OC(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC000174908411.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174908411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000174908411 none CC(C)(C)OC(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 40, 9, 40, 9, 9, 9, 9, 2, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 2, 2, 2, 9, 9] 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: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908411 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908411/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908411 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 988) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CC(C)(C)OC(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC000174908411.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174908411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908411/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000174908411 none CC(C)(C)OC(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 40, 10, 40, 10, 10, 10, 10, 2, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 2, 2, 2, 2, 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: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908411 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000174908411 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908411/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908411/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000174908411 Building ZINC000129834646 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129834646' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129834646 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000129834646 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129834646/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129834646 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/989 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)Cc2cccc(N(C)C)c2)cc1) `ZINC000129834646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000129834646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129834646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000129834646 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)Cc2cccc(N(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 11, 32, 32, 32, 32, 32, 50, 50, 32, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129834646 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129834646/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129834646 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/990 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/990' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2cccc(N(C)C)c2)cc1) `ZINC000129834646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000129834646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129834646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000129834646 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2cccc(N(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 11, 32, 32, 32, 32, 32, 50, 50, 32, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129834646 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000129834646 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129834646/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129834646/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129834646 Building ZINC000129834646 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129834646' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129834646 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000129834646 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129834646/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129834646 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 989) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/989: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)Cc2cccc(N(C)C)c2)cc1) `ZINC000129834646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000129834646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129834646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000129834646 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)Cc2cccc(N(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 11, 32, 32, 32, 32, 32, 50, 50, 32, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129834646 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129834646/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129834646 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 990) grep: /scratch/xiaobo/83235/xao-8058115.15/working/3D/990: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2cccc(N(C)C)c2)cc1) `ZINC000129834646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000129834646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129834646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000129834646 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2cccc(N(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 11, 32, 32, 32, 32, 32, 50, 50, 32, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129834646 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000129834646 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129834646/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129834646/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129834646 Building ZINC000543485901 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000543485901' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000543485901 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000543485901 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000543485901/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000543485901 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/991 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)ccc21) `ZINC000543485901.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000543485901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000543485901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000543485901 none CN1C(=O)CCc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 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, 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] 0 hydrogens need 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, 50, 50, 50, 50, 39, 9, 9, 1, 9, 1, 1, 1, 6, 6, 1, 1, 6, 6, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 6, 6, 6, 6, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000543485901 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000543485901/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000543485901 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/992 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/992' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)ccc21) `ZINC000543485901.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000543485901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000543485901/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000543485901 none CN1C(=O)CCc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 50, 50, 50, 50, 39, 9, 9, 1, 9, 1, 1, 1, 6, 6, 1, 1, 6, 6, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 6, 6, 6, 6, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000543485901 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000543485901 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000543485901/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000543485901/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000543485901 Building ZINC000543485901 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000543485901' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000543485901 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000543485901 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000543485901/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000543485901 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 991) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN1C(=O)CCc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)ccc21) `ZINC000543485901.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000543485901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000543485901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000543485901 none CN1C(=O)CCc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 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, 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] 0 hydrogens need 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, 50, 50, 50, 50, 39, 9, 9, 1, 9, 1, 1, 1, 6, 6, 1, 1, 6, 6, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 6, 6, 6, 6, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000543485901 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000543485901/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000543485901 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 992) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CN1C(=O)CCc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)ccc21) `ZINC000543485901.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000543485901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000543485901/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000543485901 none CN1C(=O)CCc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 50, 50, 50, 50, 39, 9, 9, 1, 9, 1, 1, 1, 6, 6, 1, 1, 6, 6, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 6, 6, 6, 6, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000543485901 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000543485901 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000543485901/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000543485901/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000543485901 Building ZINC000175070049 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175070049' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175070049 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175070049 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175070049/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175070049 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/993 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(C)CCC1) `ZINC000175070049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175070049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175070049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000175070049 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 18, 37, 37, 37, 37, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 2, 12, 12, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 126 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175070049 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175070049/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175070049 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/994 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/994' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(C)CCC1) `ZINC000175070049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175070049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175070049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000175070049 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 4, 21, 39, 39, 39, 39, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 4, 14, 14, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 130 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175070049 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175070049 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175070049/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175070049/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175070049 Building ZINC000175070049 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175070049' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175070049 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175070049 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175070049/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175070049 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 993) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(C)CCC1) `ZINC000175070049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175070049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175070049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000175070049 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 18, 37, 37, 37, 37, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 2, 12, 12, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 126 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175070049 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175070049/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175070049 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 994) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(C)CCC1) `ZINC000175070049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175070049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175070049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000175070049 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 4, 21, 39, 39, 39, 39, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 4, 14, 14, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 130 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175070049 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000175070049 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175070049/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175070049/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000175070049 Building ZINC000129854026 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129854026' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129854026 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000129854026 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129854026/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129854026 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/995 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccn(C3CCCC3)n2)cc1) `ZINC000129854026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000129854026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129854026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000129854026 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccn(C3CCCC3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 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: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 21, 30, 50, 50, 50, 50, 21, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129854026 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129854026/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129854026 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/996 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/996' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccn(C3CCCC3)n2)cc1) `ZINC000129854026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000129854026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129854026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000129854026 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccn(C3CCCC3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 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: [3, 2, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 20, 20, 20, 29, 50, 50, 50, 50, 20, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129854026 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000129854026 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129854026/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129854026/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129854026 Building ZINC000129854026 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129854026' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129854026 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000129854026 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129854026/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129854026 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 995) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccn(C3CCCC3)n2)cc1) `ZINC000129854026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000129854026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129854026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000129854026 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccn(C3CCCC3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 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: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 21, 30, 50, 50, 50, 50, 21, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129854026 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129854026/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129854026 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 996) grep: /scratch/xiaobo/83235/xao-8058115.15/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: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccn(C3CCCC3)n2)cc1) `ZINC000129854026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000129854026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129854026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000129854026 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccn(C3CCCC3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 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: [3, 2, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 20, 20, 20, 29, 50, 50, 50, 50, 20, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129854026 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000129854026 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129854026/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129854026/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000129854026 Building ZINC000784143149 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000784143149' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000784143149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000784143149 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000784143149/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000784143149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/997 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCCCCCCNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000784143149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000784143149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000784143149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000784143149 none CSCCCCCCNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 17, 18, 17, 11, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 38, 38, 38, 22, 22, 22, 22, 18, 18, 18, 18, 18, 18, 11, 11, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000784143149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000784143149/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000784143149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/998 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/998' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCCCCCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000784143149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000784143149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000784143149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000784143149 none CSCCCCCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 17, 18, 17, 11, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 38, 38, 38, 22, 22, 22, 22, 18, 18, 18, 18, 18, 18, 11, 11, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 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]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000784143149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000784143149 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000784143149/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000784143149/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000784143149 Building ZINC000784143149 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000784143149' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000784143149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000784143149 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000784143149/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000784143149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 997) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CSCCCCCCNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000784143149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000784143149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000784143149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000784143149 none CSCCCCCCNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 17, 18, 17, 11, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 38, 38, 38, 22, 22, 22, 22, 18, 18, 18, 18, 18, 18, 11, 11, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000784143149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000784143149/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000784143149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 998) grep: /scratch/xiaobo/83235/xao-8058115.15/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: CSCCCCCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000784143149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000784143149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000784143149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000784143149 none CSCCCCCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 17, 18, 17, 11, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 38, 38, 38, 22, 22, 22, 22, 18, 18, 18, 18, 18, 18, 11, 11, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 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]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000784143149 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000784143149 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000784143149/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000784143149/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000784143149 Building ZINC000788534787 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788534787' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788534787 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000788534787 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788534787/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788534787 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/999 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(O)(c3ccc(Cl)cc3)C2)cc1) `ZINC000788534787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000788534787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788534787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000788534787 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(O)(c3ccc(Cl)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 5, 8, 29, 29, 29, 29, 50, 50, 49, 49, 50, 50, 29, 3, 3, 3, 3, 3, 3, 3, 29, 29, 87, 50, 50, 50, 50, 29, 29, 3, 3] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 187 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788534787 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788534787/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788534787 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/83235/xao-8058115.15/working/3D/1000 `/scratch/xiaobo/83235/xao-8058115.15/working/3D/1000' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC(O)(c3ccc(Cl)cc3)C2)cc1) `ZINC000788534787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000788534787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788534787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000788534787 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC(O)(c3ccc(Cl)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 4, 7, 27, 27, 27, 27, 50, 50, 27, 38, 50, 50, 27, 3, 3, 3, 3, 3, 3, 3, 27, 27, 81, 50, 50, 50, 50, 27, 27, 3, 3] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 259 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788534787 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000788534787 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788534787/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788534787/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788534787 Building ZINC000788534787 mkdir: created directory `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788534787' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788534787 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000788534787 mkdir: created directory `0' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788534787/0 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788534787 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 0 (index: 999) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(O)(c3ccc(Cl)cc3)C2)cc1) `ZINC000788534787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000788534787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788534787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000788534787 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(O)(c3ccc(Cl)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 5, 8, 29, 29, 29, 29, 50, 50, 49, 49, 50, 50, 29, 3, 3, 3, 3, 3, 3, 3, 29, 29, 87, 50, 50, 50, 50, 29, 29, 3, 3] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 187 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788534787 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 mkdir: created directory `1' /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788534787/1 /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788534787 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Protomer 1 (index: 1000) grep: /scratch/xiaobo/83235/xao-8058115.15/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC(O)(c3ccc(Cl)cc3)C2)cc1) `ZINC000788534787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000788534787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788534787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000788534787 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC(O)(c3ccc(Cl)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 4, 7, 27, 27, 27, 27, 50, 50, 27, 38, 50, 50, 27, 3, 3, 3, 3, 3, 3, 3, 27, 27, 81, 50, 50, 50, 50, 27, 27, 3, 3] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 259 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788534787 /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Finished preparing ZINC000788534787 Recording results /scratch/xiaobo/83235/xao-8058115.15/working /scratch/xiaobo/83235/xao-8058115.15 Appending to /scratch/xiaobo/83235/xao-8058115.15/finished/xao.* 1: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788534787/1.* 0: /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788534787/0.* Removing working files in /scratch/xiaobo/83235/xao-8058115.15/working/building/ZINC000788534787 /scratch/xiaobo/83235/xao-8058115.15 Compressing combined databse files /scratch/xiaobo/83235/xao-8058115.15/finished/xao.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/83235/xao-8058115.15/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/83235/xao-8058115.15/working/3D/1001' removed directory: `/scratch/xiaobo/83235/xao-8058115.15/working/3D' rmdir: removing directory, `/scratch/xiaobo/83235/xao-8058115.15/working/building' rmdir: removing directory, `/scratch/xiaobo/83235/xao-8058115.15/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/logs `/scratch/xiaobo/83235/xao-8058115.15' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xao' `/scratch/xiaobo/83235/xao-8058115.15/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xao/finished' `/scratch/xiaobo/83235/xao-8058115.15/finished/xao.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xao/finished/xao.db2.gz' removed `/scratch/xiaobo/83235/xao-8058115.15/finished/xao.db2.gz' removed directory: `/scratch/xiaobo/83235/xao-8058115.15/finished' removed directory: `/scratch/xiaobo/83235/xao-8058115.15'